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cgi-updater/cgi-updater-payload.sh
Go to file| #!/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 |