singularity/Singularity.R

In biomics-pasteur-fr/RNADiff: R Tools for RNA-Seq Projects at Institut Pasteur (Biomics Platform)

Bootstrap: docker
From: ubuntu:16.04


%labels
    Author thomas cokelaer
    Version v1.0

%post

    # Software versions
    export R_VERSION=3.6.1

    # Get dependencies
    apt-get update
    apt-get install -y --no-install-recommends locales
    apt-get install -y git

    # prevents warnings
    export DEBIAN_FRONTEND=noninteractive

    # Configure default locale
    echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
    locale-gen en_US.utf8
    /usr/sbin/update-locale LANG=en_US.UTF-8
    export LC_ALL=en_US.UTF-8
    export LANG=en_US.UTF-8

    # Install R
    echo "deb http://cran.r-project.org/bin/linux/ubuntu xenial-cran35/" > /etc/apt/sources.list.d/r.list
    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
    apt-get update
    apt-key update
    apt-get install -y --no-install-recommends --allow-unauthenticated \
      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 \

    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/*

    # Install devtools
	echo ' chooseCRANmirror(ind=26)' >> runme.R
    echo ' install.packages("devtools")' >> runme.R
    Rscript runme.R



%environment
    export LC_ALL=en_US.UTF-8
    export LANG=en_US.UTF-8
    export PATH=$PATH:/usr/bin