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Singularity.def
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Singularity.def
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Bootstrap: docker
From: debian:bookworm
%post
apt update
apt upgrade -y
apt install -y eatmydata # https://manpages.debian.org/eatmydata
ln -s /usr/bin/eatmydata ./apt
ln -s /usr/bin/eatmydata ./R
./apt install -y locales
sed -i /etc/locale.gen -e '/en_[UG].*.UTF-8/s/# //'
locale-gen
./apt install -y pandoc qpdf texlive # For vignette builds and package checks
./apt install -y cmake libxml2-dev libcurl4-openssl-dev libssl-dev libfftw3-dev libtiff-dev libgsl-dev
./apt install -y libfontconfig1-dev libharfbuzz-dev libfribidi-dev # For pkgdown
./apt install -y libproj-dev # For proj4, for ggmsa
./apt install -y bash-completion file sudo wget htop strace
./apt install -y last-align # For maf-convert
./apt install -y r-base r-base-dev
./R -e 'install.packages("BiocManager")'
./R -e 'install.packages("tidyverse")'
./R -e 'install.packages("devtools")'
./R -e 'install.packages("remotes")'
./R -e 'install.packages("rmarkdown")'
./R -e 'BiocManager::install("GenomicRanges")'
./R -e 'remotes::install_github("oist/GenomicBreaks", repos=BiocManager::repositories(), dependencies=TRUE)'
printf 'R_LIBS_SITE="/usr/local/lib/R/site-library:/usr/lib/R/library\n' | tee -a /etc/R/Renviron.site >/dev/null
printf 'R_LIBS_USER="~/R/library/GBreaks_singularity_0.14\n' | tee -a /etc/R/Renviron.site >/dev/null
rm ./apt ./R