Commit 504bd6de authored by Valentin Vautrot's avatar Valentin Vautrot

Implementation of a singularity definition file to contain R with affymetrix package

parent 6817ed5c
BootStrap: docker
From: ubuntu:22.04
%help
This is a singularity container packing R version 4.4.0 and all the dependencies necessary to run the affy package from affymetrix, in order to process .cel transcriptomics files
run the command 'apptainer test <image_name>.sif' to see the actual versions of R and "affy" package installed
built-in R packages should be located in /usr/lib/R/library
other R packages should be located in /usr/local/lib/R/site-library
Authors : valentin.vautrot@u-bourgogne.fr
%post
# export R_VERSION=4.3.3
# 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 language-pack-fr 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 jammy-cran40/"
apt-get install -y --no-upgrade --no-install-recommends -t jammy-cran40 r-base-core=4.4.0-1.2204.0 r-base=4.4.0-1.2204.0 r-recommended=4.4.0-1.2204.0 r-base-dev=4.4.0-1.2204.0
apt-get install -y --no-upgrade --no-install-recommends build-essential libcurl4-openssl-dev zlib1g-dev libxml2-dev libssl-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libbz2-dev gfortran
echo "installed R version :"
R --version
# # install R packages :
# Rscript -e 'install.packages("devtools")'
Rscript -e 'install.packages("BiocManager", dependencies=TRUE)'
Rscript -e 'BiocManager::install("Biobase", version = "3.19")'
Rscript -e 'BiocManager::install("affy", version = "3.19")'
# Clean up
rm -rf /var/lib/apt/lists/*
%environment
export LANGUAGE=fr_FR.UTF-8
export LC_ALL=fr_FR.UTF-8
export LANG=fr_FR.UTF-8
export LC_CTYPE=fr_FR.UTF-8
%test
echo "installed R version :"
R --version
echo "installed affy package version :"
Rscript -e 'packageVersion("affy")'
%labels
Auhtors valentin.vautrot@u-bourgogne.fr
Contained_OS_version Ubuntu_22.04_LTS_JammyJellyfish
Contained_R_version 4.4.0
Contained_FRASER_version 1.14.1
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