cgi-updater-payload.sh

#!/bin/bash

r_pkgs=( DESeq2 grDevices genefilter biomaRt ggplot2 gplots RColorBrewer )
pip_pkgs=( biopython )

if [[ $(id -u) -ne 0 ]]; then
    echo "Error: run this script as the root user, not EUID $(id -u)."
    exit 1
fi

set -e				# Make most errors fatal.

ubuntu_update () {
    apt-get update
    apt-get -y upgrade
}

ubuntu_install_r_cran () {
    cat <<EOF > /etc/apt/sources.list.d/cgi-r-cran.list
# Newest R version from CRAN per
# https://cran.r-project.org/bin/linux/ubuntu/
deb https://cran.fhcrc.org/bin/linux/ubuntu $(lsb_release -cs)/
EOF
    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
    apt-get update
    apt-get -y install r-base-dev
}

python_install_packages() {
    pip install --upgrade ${pip_pkgs[@]}
}

r_install_packages() {
    local pkgs=\"$(sprintf "\",%s\"" "${r_pkgs[@]}")\"
    R --quiet -vanilla -e <<EOF
source("https://bioconductor.org/biocLite.R")
biocLite(c(${pkgs:3})
EOF
}

main () {
    ubuntu_update
    ubuntu_install_r_cran

    python_install_packages
    
    # Install R libraries in the user home directory so that updating
    # the libraries later on does not triggering the "unwritable
    # directory" warning.
    export r_pkgs
    export -f r_install packages
    su cgi_user -c "bash -c r_install_packages"
    unset r_pkgs r_install_packages
}

main