R_4.4.0_affymetrix.def

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 oligo and limma packages for microarray data treatment, in order to process .cel transcriptomics files from mouse Clariom S affymetrix arrays.
Run the command 'apptainer test <image_name>.sif' to see the actual versions of R and other packages 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-cran-mass=7.3-60-2.2204.0 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("BiocManager", dependencies=TRUE)'
Rscript -e 'BiocManager::install("Biobase", version = "3.19")'
Rscript -e 'BiocManager::install("oligo", version = "3.19")'
Rscript -e 'BiocManager::install("affy", version = "3.19")'
Rscript -e 'BiocManager::install("pd.clariom.s.mouse", version = "3.19")'
Rscript -e 'BiocManager::install("limma", version = "3.19")'
Rscript -e 'BiocManager::install("gcrma", version = "3.19")'
Rscript -e 'BiocManager::install("biomaRt", version = "3.19")'
Rscript -e 'BiocManager::install("affycoretools", version = "3.19")'

Rscript -e 'install.packages("ggrepel")'
Rscript -e 'install.packages("tidyverse")'

# 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 oligo package version :"
Rscript -e 'packageVersion("oligo")'
echo "installed affy package version :"
Rscript -e 'packageVersion("oligo")'
echo "annotation package pd.clariom.s.mouse :"
Rscript -e 'packageVersion("pd.clariom.s.mouse")'
echo "installed limma version :"
Rscript -e 'packageVersion("limma")'
echo "installed gcrma version :"
Rscript -e 'packageVersion("gcrma")'
echo "installed biomaRt version :"
Rscript -e 'packageVersion("biomaRt")'
echo "installed affycoretools version :"
Rscript -e 'packageVersion("affycoretools")'

%labels 
Auhtors valentin.vautrot@u-bourgogne.fr
Contained_OS_version Ubuntu_22.04_LTS_JammyJellyfish
Contained_R_version 4.4.0