bioconductor

#!/bin/bash

## version is RELEASE_X_Y
version=$1
## either rstudio or bash
envtype=$2
## defaults to 8787
port=$3

GVER=`echo "$version" | grep -E "^[3-4]\.[0-9]{1,2}.*"`

if [ -z "${version// }" ] || [[ $version != RELEASE_* ]] && ([[ $version != devel* ]] && [ -z "${GVER// }" ]); then
    echo "Enter either 'devel*', 'X.Y', or 'RELEASE_X_Y' version"
    exit 1
fi

if [ -z "${envtype// }" ]; then
    echo "Empty 'envtype' using default: rstudio"
    envtype="rstudio"
elif [ $envtype == "shell" ]; then
    envtype="bash"
fi

if [[ $envtype != "rstudio" && $envtype != "bash" ]]; then
    echo "Enter either 'rstudio' or 'bash' environment type"
    exit 2
fi

if [ -z "${port// }" ]; then
    port=8787
fi

biocdocker=bioconductor/bioconductor_docker:"$version"

docker pull $biocdocker

DOCKER_RPKGS="$HOME/.docker-$version-packages"
DOCKER_HOME="$HOME/dockerhome"
R_LIBS='/usr/local/lib/R/host-site-library:/usr/local/lib/R/site-library:/usr/local/lib/R/library'

mkdir -p "$DOCKER_RPKGS"
mkdir -p "$DOCKER_HOME"

if [ ! -f "$DOCKER_HOME"/.Renviron ]; then
    echo "R_LIBS=$R_LIBS" > $DOCKER_HOME/.Renviron
fi

TOKEN_EXP='GITHUB_[P|T].*'

GPAT=`grep "$TOKEN_EXP" ~/.Renviron`
GRENV=`grep "$TOKEN_EXP" $DOCKER_HOME/.Renviron`

if [ ! -z "${GPAT// }" ] && [ -z "${GRENV// }" ]; then
    echo $GPAT >> $DOCKER_HOME/.Renviron
fi

HLIBUSER=`grep "R_LIBS_USER" ~/.Renviron`

if [ -z "${HLIBENV// }" ]; then
    echo "R_LIBS_USER=/usr/local/lib/R/host-site-library" >> $DOCKER_HOME/.Renviron
fi

copy_config() {
    for arg in "$@"; do
        FILE="$HOME/$arg"
        if [ -e ${FILE} ] && [ ! -e $DOCKER_HOME/$arg ]; then
            cat $FILE > $DOCKER_HOME/$arg
        fi
    done
}

copy_config .Rprofile .gitconfig .inputrc

echo "Installed packages will go in host directory: $DOCKER_RPKGS"
echo "RStudio home directory will be mounted on host directory: $DOCKER_HOME"
echo $envtype

if [ $envtype == "rstudio" ]; then
    echo "Open RStudio running Bioconductor version $version at http://localhost:$port"
fi

if [ $envtype == "rstudio" ]; then
    docker run -e PASSWORD=bioc \
        -v $DOCKER_HOME:/home/rstudio \
        -v $DOCKER_RPKGS:/usr/local/lib/R/host-site-library \
        -e USERID=$UID \
        -p $port:8787 \
        $biocdocker \
        bash -c 'chown -R rstudio /home/rstudio; chown -R rstudio /usr/local/lib/R/host-site-library; /init'
elif [ $envtype == "bash" ]; then
    docker run -ti --user rstudio \
        -v $DOCKER_HOME:/home/rstudio \
        -v $DOCKER_RPKGS:/usr/local/lib/R/host-site-library \
        -w /home/rstudio \
        $biocdocker bash
fi