Commit 2d5aaa5b authored by Valentin Vautrot's avatar Valentin Vautrot

Initial implementation of R definition file to run R program for mouse chipseq…

Initial implementation of R definition file to run R program for mouse chipseq analysis (chipseq_mm10.R)
parent ffa4d431
BootStrap: docker
From: ubuntu:22.04
%help
This is a singularity container packing R version 4.3.3 [at the time of build] and all the dependencies necessary to run chipSeq_mm10.R (ChipSeq results annotation for mouse).
(BiocManager version : 3.18)
run the command 'apptainer test <image_name>.sif' to test the image and check the actual version of R installed
built-in R packages are installed in /usr/lib/R/library
other R packages were added in /usr/local/lib/R/site-library
Authors : valentin.vautrot@u-bourgogne.fr
#TODO : R version control
%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 \
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-install-recommends -t jammy-cran40 r-base r-recommended r-base-dev
apt-get install -y --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 libmagick++-dev
# # install R packages :
# CRAN
Rscript -e 'install.packages("devtools")'
Rscript -e 'devtools::install_version("ggimage", version ="0.3.0", repos = "https://cran.r-project.org")'
Rscript -e 'devtools::install_version("vegan", version ="2.6-4", repos = "https://cran.r-project.org")'
Rscript -e 'devtools::install_version("RcppArmadillo", version ="0.12.8.1.0", repos = "https://cran.r-project.org")'
Rscript -e 'devtools::install_version("UpSetR", version ="1.4.0", repos = "https://cran.r-project.org")'
Rscript -e 'devtools::install_version("ggupset", version ="0.3.0", repos = "https://cran.r-project.org")'
# bioconductor
Rscript -e 'install.packages("BiocManager", dependencies=TRUE)'
Rscript -e 'BiocManager::install("ChIPseeker", version = "3.18")'
Rscript -e 'BiocManager::install("GenomicFeatures", version = "3.18")'
Rscript -e 'BiocManager::install("clusterProfiler", version = "3.18")'
Rscript -e 'BiocManager::install("ReactomePA", version = "3.18")'
Rscript -e 'BiocManager::install("TxDb.Mmusculus.UCSC.mm10.knownGene", version = "3.18")'
# others
Rscript -e 'devtools::install_github("stephenturner/annotables", version="0.1.90")'
# Clean up
rm -rf /var/lib/apt/lists/*
%test
echo "installed R version :"
R --version
echo "installed BiocManager version for bioconductor packages :"
Rscript -e "BiocManager::version()"
%labels
Auhtors valentin.vautrot@u-bourgogne.fr
Contained_OS_version Ubuntu_22.04_LTS_JammyJellyfish
Contained_R_version 4.3.3
Contained_BiocManager_version 3.18
\ No newline at end of file
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