Adding R3.4 singularity definition

R_3.4.def

+BootStrap: docker
+From: ubuntu:20.04
+
+%labels
+  Maintainer Jeremy Nicklas
+  R_Version 4.2.1
+
+%apprun R
+  exec R "${@}"
+
+%apprun Rscript
+  exec Rscript "${@}"
+
+%runscript
+  exec R "${@}"
+
+%post
+  # Software versions
+  export R_VERSION=4.3.1
+  echo "export R_VERSION=${R_VERSION}" >> $SINGULARITY_ENVIRONMENT
+
+  # Get dependencies
+  apt-get update
+  apt-get install -y --no-install-recommends \
+    locales
+
+
+  # Install R
+  apt-get update
+  apt-get install -y --no-install-recommends \
+    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 $(lsb_release -cs)-cran40/"
+  apt-get install -y --no-install-recommends \
+    r-base=${R_VERSION}* \
+    r-base-core=${R_VERSION}* \
+    r-base-dev=${R_VERSION}* \
+    r-recommended=${R_VERSION}* \
+    r-base-html=${R_VERSION}* \
+    r-doc-html=${R_VERSION}* \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    libxml2-dev \
+    libcairo2-dev \
+    libxt-dev \
+    libopenblas-dev
+
+  # Add a default CRAN mirror
+  echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/lib/R/etc/Rprofile.site
+
+  # Add a directory for host R libraries
+  mkdir -p /library
+  echo "R_LIBS_SITE=/library:\${R_LIBS_SITE}" >> /usr/lib/R/etc/Renviron.site
+
+  # Clean up
+  rm -rf /var/lib/apt/lists/*
+
+  # add R libs :
+  # bioconductor
+  Rscript -e 'install.packages("BiocManager" , dependencies=TRUE)'
+  # Rscript -e 'install.packages("devtools")'
+  Rscript -e 'install.packages("gghighlight")'
+  Rscript -e 'install.packages("ggfortify")'
+  Rscript -e 'install.packages("RColorBrewer")'
+  Rscript -e 'install.packages("pheatmap")'
+  Rscript -e 'install.packages("tidyverse")'
+  Rscript -e 'install.packages("ggplot2")'
+
+
+  Rscript -e 'BiocManager::install("DESeq2")'
+  Rscript -e 'BiocManager::install("limma")'
+  Rscript -e 'BiocManager::install("edgeR")'
+  Rscript -e 'BiocManager::install("limma")'
+  Rscript -e 'BiocManager::install("mixOmics")'
+  Rscript -e 'BiocManager::install("HTSFilter")'
+  # Rscript -e 'devtools::install_github("yanlinlin82/ggvenn")'
+
+%test
+
+R --quiet -e "stopifnot(getRversion() == '${R_VERSION}')"