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gad-public
singularity
Commits
18ad533c
Commit
18ad533c
authored
1 year ago
by
Valentin Vautrot
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Create definition file for singularity image dedicated to R analysis using OUTRIDER
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18ad533c
BootStrap: docker
From: ubuntu:18.04
%help
This is a singularity container packing R version 3.6.3 and all the dependencies necessary to run the outrider ("Outlier in rnaseq finder") package, version 1.4.2, for rnaseq analysis.
(BiocManager version : 3.10)
Authors : valentin.vautrot@u-bourgogne.fr
%apprun R
exec R "${@}"
%apprun Rscript
exec Rscript "${@}"
%runscript
exec R "${@}"
%post
export R_VERSION=3.6.3
echo "export R_VERSION=${R_VERSION}" >> $SINGULARITY_ENVIRONMENT
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install -y --no-install-recommends apt-utils
apt-get install -y --no-install-recommends \
locales \
software-properties-common \
dirmngr \
wget \
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
# add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/"
add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/"
apt update
apt-get install -y --no-install-recommends -t bionic-cran35 r-base=${R_VERSION}-1bionic r-recommended=${R_VERSION}-1bionic r-base-core=${R_VERSION}-1bionic r-base-dev=${R_VERSION}-1bionic r-base-html=${R_VERSION}-1bionic r-doc-html=${R_VERSION}-1bionic
apt-get install -y --no-install-recommends libcurl4-openssl-dev libxml2-dev libssl-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
# libcairo2-dev \
# libxt-dev \
# libopenblas-dev
# # Add a directory for host R libraries
# mkdir -p /library
# echo "R_LIBS_SITE=/library:\${R_LIBS_SITE}" >> /usr/lib/R/etc/Renviron.site
# install R packages :
Rscript -e 'install.packages("devtools")'
Rscript -e 'devtools::install_version("XML", version ="3.98.1.20", repos = "https://cran.r-project.org")'
Rscript -e 'devtools::install_version("htmlTable", version ="1.13.3", repos = "https://cran.r-project.org")'
Rscript -e 'devtools::install_version("locfit", version ="1.5.9.1", repos = "https://cran.r-project.org")'
Rscript -e 'devtools::install_version("Hmisc", version ="4.3.0", repos = "https://cran.r-project.org")'
Rscript -e 'install.packages("BiocManager", dependencies=TRUE)'
Rscript -e 'BiocManager::install("OUTRIDER", version = "3.10")'
# # Clean up
# rm -rf /var/lib/apt/lists/*
# %test
# R --quiet -e "stopifnot(getRversion() == '${R_VERSION}')"
\ No newline at end of file
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