Create definition file for singularity image dedicated to R analysis using OUTRIDER

R_3.6_outrider.def

+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}')"
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