Merge branch 'release/v4.2.0'

cancerit · Mar 9, 2018 · e20cfbd · e20cfbd
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,14 +1,29 @@
-### 4.1.1
+# Changes
+
+## 4.2.0
+
+* Upgrade to core R [ASCAT v2.5.1](https://github.com/Crick-CancerGenomics/ascat/releases/tag/v2.5)
+  * applies patch to handle sparse data on a contig (usually Human Y)
+* Recommend upgrading to [alleleCount v4.0.0+](https://github.com/cancerit/alleleCount/releases)
+  * Switches to fragment based counts instead of read based to prevent double counting.
+
+## 4.1.1
+
 * Fix error in setup.sh testing of alleleCounter version
 
-### 4.1.0
+## 4.1.0
+
 * Modified to use new >= 3.3.0 allelecounter code with dense SNP functionality
 
-### 2.1.2
+## 2.1.2
+
 * Minor fix to usage typo
 
-### 2.0.0
-* Now species agnostic provided you can generate a panel of SNPs, approx 1 HET per 2kb is required.  Tools are included in the package for guided and unguided SNP generation.  More details can be found in the [wiki](https://github.com/cancerit/ascatNgs/wiki).
+## 2.0.0
+
+* Now species agnostic provided you can generate a panel of SNPs, approx 1 HET per 2kb is required.
+  * Tools are included in the package for guided and unguided SNP generation.
+  * More details can be found in the [wiki](https://github.com/cancerit/ascatNgs/wiki).
 * Supports CRAM
 * Allele count phase is now threaded.
 

diff --git a/README.md b/README.md
@@ -1,69 +1,110 @@
-AscatNGS
-========
+# AscatNGS
+
+| Master                                        | Develop                                         |
+| --------------------------------------------- | ----------------------------------------------- |
+| [![Master Badge][travis-master]][travis-base] | [![Develop Badge][travis-develop]][travis-base] |
+
 AscatNGS contains the Cancer Genome Projects workflow implementation of the ASCAT copy number
 algorithm for paired end sequencing.
 
-##For WHOLEGENOME (WGS) sequencing only
-We do not offer support for WXS analysis, please contact the authors of [ASCAT](https://www.crick.ac.uk/peter-van-loo/software/ASCAT).
+**_We do not offer support for WXS analysis, please contact the authors of ASCAT [here][ascat-web]_**.
+
+For details of the underlying algorithm please see the [ASCAT][ascat-web] site.  The GitHub
+repository can be found [here][ascat-gh].
+
+Contents:
+
+<!-- TOC depthFrom:2 depthTo:6 withLinks:1 updateOnSave:1 orderedList:0 -->
+
+- [ASCAT core algorithm](#ascat-core-algorithm)
+- [Docker, Singularity and Dockstore](#docker-singularity-and-dockstore)
+- [Dependencies/Install](#dependenciesinstall)
+	- [Reference files](#reference-files)
+- [Creating a release](#creating-a-release)
+	- [Preparation](#preparation)
+	- [Cutting the release](#cutting-the-release)
+- [LICENCE](#licence)
+
+<!-- /TOC -->
+
+## ASCAT core algorithm
 
----
+The core `ascat.R` script is pulled from the primary ASCAT repository during installation.  The
+linked version is currently [`v2.5.1`][ascat-release].
 
-For details of the underlying algorithm please see the [ASCAT](https://www.crick.ac.uk/peter-van-loo/software/ASCAT) site.  The GitHub repoitory can be found [here](https://github.com/Crick-CancerGenomics/ascat).
+### Minimum sequence depth
 
-| Master | Dev |
-|---|---|
-| [![Master Build Status](https://travis-ci.org/cancerit/ascatNgs.svg?branch=master)](https://travis-ci.org/cancerit/ascatNgs) | [![Dev Build Status](https://travis-ci.org/cancerit/ascatNgs.svg?branch=dev)](https://travis-ci.org/cancerit/ascatNgs) |
+The minimum depth that you are likely to get reliable results from is 15x genome coverage.  If you
+have very good quality data with good insert size (little or no overlap of reads) you may be successful
+with 12x.
 
----
+## Docker, Singularity and Dockstore
 
-### ASCAT core algorithm
-The core `ascat.R` script is pulled from the primary ASCAT repository during intallation.  The linked version is currently [`v2.4.3`](https://github.com/Crick-CancerGenomics/ascat/releases/tag/v2.4.3).
+There is a pre-built image containing this codebase on quay.io.
+
+* [dockstore-cgpwgs][ds-cgpwgs-git]: Contains additional tools for WGS analysis.
+
+This was primarily designed for use with dockstore.org but can be used as normal containers.
+
+The docker images are know to work correctly after import into a singularity image.
+
+## Dependencies/Install
 
-###Dependencies/Install
 Please install the following first:
 
-* [PCAP-core v2.0+](http://github.com/ICGC-TCGA-PanCancer/PCAP-core/releases)
+* [PCAP-core v2.0+][pcap-core-rel]
   * `ascatNgs` has other dependancies fulfilled by `PCAP-core`.
-* [cgpVcf v2.0+](https://github.com/cancerit/cgpVcf/releases)
-* [alleleCount v3.0+](https://github.com/cancerit/alleleCount/releases)
+* [cgpVcf v2.0+][cgpvcf-rel]
+* alleleCount
+  * [alleleCount v4.0.0+][allelecount-rel] - for fragment based counting (recommended)
+  * [alleleCount v3.0.0 - v3.3.1][allelecount-v3] - for read based counting
+* [RColorBrewer][rcolorbrewer]
 
 Please see these for any child dependencies.
 
 Once complete please run:
 
+```
 ./setup.sh /some/install/location
+```
 
-If you are installing each tool (PCAP-code, cgpVcf, alleleCount) to an independent area you should set the environment variable `CGP_PERLLIBS` to include the relevant perl libraries from those.
+If you are installing each tool (`PCAP-code`, `cgpVcf`, `alleleCount`) to an independent area you should
+set the environment variable `CGP_PERLLIBS` to include the relevant perl libraries from those, e.g.
+
+```
+export CGP_PERLLIBS=/pcapInst/libs/perl5:/cgpvcfInst/libs/perl5:...
+```
 
 Please be aware that this software requires the Rscript executable to be pre-installed.
 
 ### Reference files
 
-Please see the [wiki](https://github.com/cancerit/ascatNgs/wiki) for how to obtain/generate the `SnpGcCorrections.tsv` file.
+Please see the [wiki][ascatngs-wiki] for how to obtain/generate the
+`SnpGcCorrections.tsv` file.
+
+## Creating a release
 
----
+### Preparation
 
-##Creating a release
-####Preparation
 * Commit/push all relevant changes.
 * Pull a clean version of the repo and use this for the following steps.
 
-####Cutting the release
+### Cutting the release
+
 1. Update `perl/lib/Sanger/CGP/Ascat.pm` to the correct version.
-2. Update `CHANGES.md` with key updates.
-3. Run `./prerelease.sh`
-4. Check all tests and coverage reports are acceptable.
-5. Commit the updated docs tree and updated module/version.
-6. Push commits.
-7. Use the GitHub tools to draft a release.
+1. Update `CHANGES.md` with key updates.
+1. Run `./prerelease.sh`
+1. Check all tests and coverage reports are acceptable.
+1. Commit the updated docs tree and updated module/version.
+1. Push commits.
+1. Use the GitHub tools to draft a release.
 
----
+## LICENCE
 
-LICENCE
-========
-Copyright (c) 2014-2016 Genome Research Ltd.
+```
+Copyright (c) 2014-2018 Genome Research Ltd.
 
-Author: CancerIT <cgpit@sanger.ac.uk>
+Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 
 This file is part of AscatNGS.
 
@@ -79,3 +120,21 @@ details.
 
 You should have received a copy of the GNU Affero General Public License
 along with this program. If not, see <http://www.gnu.org/licenses/>.
+```
+
+<!-- Travis -->
+[travis-base]: https://travis-ci.org/cancerit/ascatNgs
+[travis-master]: https://travis-ci.org/cancerit/ascatNgs.svg?branch=master
+[travis-develop]: https://travis-ci.org/cancerit/ascatNgs.svg?branch=dev
+
+<!-- refs -->
+[allelecount-v3]: https://github.com/cancerit/alleleCount/releases/tag/v3.3.1
+[allelecount-rel]: https://github.com/cancerit/alleleCount/releases
+[cgpvcf-rel]: https://github.com/cancerit/cgpVcf/releases
+[pcap-core-rel]: https://github.com/cancerit/PCAP-core/releases
+[ascat-web]: https://www.crick.ac.uk/peter-van-loo/software/ASCAT
+[ascat-gh]: https://github.com/Crick-CancerGenomics/ascat
+[ascat-release]: https://github.com/Crick-CancerGenomics/ascat/releases/tag/v2.5
+[ascatngs-wiki]: https://github.com/cancerit/ascatNgs/wiki
+[ds-cgpwgs-git]: https://github.com/cancerit/dockstore-cgpwgs
+[rcolorbrewer]: https://cran.r-project.org/web/packages/RColorBrewer/index.html
diff --git a/perl/Makefile.PL b/perl/Makefile.PL
@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ########## LICENCE ##########
-# Copyright (c) 2014-16 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: CancerIT <cgpit@sanger.ac.uk>
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 #
 # This file is part of AscatNGS.
 #

diff --git a/perl/bin/ascat.pl b/perl/bin/ascat.pl
@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2016 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: CancerIT <cgpit@sanger.ac.uk>
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 #
 # This file is part of AscatNGS.
 #

diff --git a/perl/bin/ascatCnToVCF.pl b/perl/bin/ascatCnToVCF.pl
@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2016 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: David Jones <cgpit@sanger.ac.uk>
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 #
 # This file is part of ascatNgs.
 #

diff --git a/perl/bin/ascatFailedCnCsv.pl b/perl/bin/ascatFailedCnCsv.pl
@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-16 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: David Jones <cgpit@sanger.ac.uk>
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 #
 # This file is part of ascatNgs.
 #

diff --git a/perl/bin/ascatToBigWig.pl b/perl/bin/ascatToBigWig.pl
@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2016 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: CancerIT <cgpit@sanger.ac.uk>
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 #
 # This file is part of AscatNGS.
 #

diff --git a/perl/bin/utilities/ascatFaiChunk.pl b/perl/bin/utilities/ascatFaiChunk.pl
@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2016 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: CancerIT <cgpit@sanger.ac.uk>
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 #
 # This file is part of AscatNGS.
 #

diff --git a/perl/bin/utilities/ascatSnpPanelFromVcfs.pl b/perl/bin/utilities/ascatSnpPanelFromVcfs.pl
@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2016 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: CancerIT <cgpit@sanger.ac.uk>
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 #
 # This file is part of AscatNGS.
 #

diff --git a/perl/bin/utilities/ascatSnpPanelGcCorrections.pl b/perl/bin/utilities/ascatSnpPanelGcCorrections.pl
@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2016 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: CancerIT <cgpit@sanger.ac.uk>
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 #
 # This file is part of AscatNGS.
 #

diff --git a/perl/bin/utilities/ascatSnpPanelGenerator.pl b/perl/bin/utilities/ascatSnpPanelGenerator.pl
@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ########## LICENCE ##########
-# Copyright (c) 2014-16 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: CancerIT <cgpit@sanger.ac.uk>
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 #
 # This file is part of AscatNGS.
 #

diff --git a/perl/bin/utilities/ascatSnpPanelMerge.pl b/perl/bin/utilities/ascatSnpPanelMerge.pl
@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ########## LICENCE ##########
-# Copyright (c) 2014-16 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: CancerIT <cgpit@sanger.ac.uk>
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 #
 # This file is part of AscatNGS.
 #

diff --git a/perl/docs.tar.gz b/perl/docs.tar.gz
diff --git a/perl/lib/Sanger/CGP/Ascat.pm b/perl/lib/Sanger/CGP/Ascat.pm
@@ -1,7 +1,7 @@
 ##########LICENCE##########
-# Copyright (c) 2014-2016 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: CancerIT <cgpit@sanger.ac.uk>
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 #
 # This file is part of AscatNGS.
 #
@@ -26,14 +26,14 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '4.1.1';
+our $VERSION = '4.2.0';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>
 '##########LICENCE##########
-# Copyright (c) 2014-2017 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: CancerIT <cgpit@sanger.ac.uk>
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 #
 # This file is part of AscatNGS.
 #

diff --git a/perl/lib/Sanger/CGP/Ascat/Implement.pm b/perl/lib/Sanger/CGP/Ascat/Implement.pm
@@ -1,7 +1,7 @@
 ##########LICENCE##########
-# Copyright (c) 2014-2017 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: CancerIT <cgpit@sanger.ac.uk>
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 #
 # This file is part of AscatNGS.
 #

diff --git a/perl/share/ascat/runASCAT.R b/perl/share/ascat/runASCAT.R
@@ -1,7 +1,7 @@
 ##########LICENCE##########
-# Copyright (c) 2014 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: Peter Van Loo <cgpit@sanger.ac.uk>
+# Author: Peter Van Loo <cgphelp@sanger.ac.uk>
 #
 # This file is part of AscatNGS.
 #
@@ -289,5 +289,3 @@ rm(refCN)
 save.image(rdat_out)
 
 q(save="no")
-
-
diff --git a/perl/t/1_pm_compile.t b/perl/t/1_pm_compile.t
@@ -1,7 +1,7 @@
 ########## LICENCE ##########
-# Copyright (c) 2014 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: CancerIT <cgpit@sanger.ac.uk>
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 #
 # This file is part of AscatNGS.
 #

diff --git a/perl/t/2_pl_compile.t b/perl/t/2_pl_compile.t
@@ -1,7 +1,7 @@
 ########## LICENCE ##########
-# Copyright (c) 2014 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: CancerIT <cgpit@sanger.ac.uk>
+# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 #
 # This file is part of AscatNGS.
 #