cgi-updater-payload.sh

#!/bin/bash

r_pkgs=( DESeq2 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
    local key=E084DAB9
    grep -q $key <( apt-key list ) ||
	apt-key adv --keyserver keyserver.ubuntu.com --recv-keys $key
    apt-get update
    apt-get -y install r-base-dev
    # Dependencies of RCurl:
    apt-get -y install libxml2-dev libcurl4-gnutls-dev
}

python_install_packages() {
    apt-get -y install python-pip python-dev
    pip install --upgrade ${pip_pkgs[@]}
}

r_install_packages() {
    local pkgs=$@
    pkgs=\"$(printf "\",\"%s" $pkgs)\"
    Rscript --vanilla - <<EOF
options(echo = TRUE)
dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)
.libPaths(Sys.getenv("R_LIBS_USER"))
setwd(paste(Sys.getenv("R_HOME")))
source("https://bioconductor.org/biocLite.R")
biocLite(c(${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 -f r_install_packages
    su cgi_user -c "bash -c \"r_install_packages ${r_pkgs[*]}\""
    unset r_install_packages
}

main