singularity.def

Bootstrap: library
From: ubuntu:18.04 

%setup

%files
    scripts/install_packages.R /tmp/install_packages.R

%environment
    # Needed for R 
    export TZ=Europe/Minsk
    # Set the locale so the shell wont complain
    export LANG=C.UTF-8
    export LC_ALL=C.UTF-8

%post

    # add the universe repo
    apt-get install software-properties-common --yes
    add-apt-repository universe 
    
    # add key and r repo
    apt-get install --yes gnupg
    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
    add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
    
    # update and install essentials
    apt-get update && apt-get upgrade --yes
    apt-get install curl wget \
        gcc \
        build-essential \
        libboost-all-dev libgsl0-dev \
        libcurl4-openssl-dev libssl-dev libxml2-dev \
        unzip less --yes

    # install R  
    ln -snf /usr/share/zoneinfo/$TZ /etc/localtime
    echo $TZ > /etc/timezone
    apt-get install r-base-dev --yes
    rm /etc/localtime

    # Install R packages
    wget https://cran.r-project.org/src/contrib/Archive/synbreed/synbreed_0.12-9.tar.gz
    wget https://cran.r-project.org/src/contrib/Archive/regress/regress_1.3-15.tar.gz
    wget https://cran.r-project.org/src/contrib/Archive/GenABEL/GenABEL_1.8-0.tar.gz
    wget https://cran.r-project.org/src/contrib/Archive/GenABEL.data/GenABEL.data_1.0.0.tar.gz
    wget http://lrgpr.r-forge.r-project.org/docs/lrgpr_0.1.12.tar.gz
    Rscript /tmp/install_packages.R