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

R_4.3.3_ChipSeq_mouse.def

+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 
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