bioconductor

#!/bin/bash
show_help() {
    echo "Usage: bioconductor.sh [-v version] [-e envtype] [-p port] [-w password] [-d dockerhome] [-l] [-h]"
    echo "  -v version    Specify the Bioconductor version (e.g., 'devel', 'RELEASE_X_Y', 'X.Y')."
    echo "  -e envtype    Specify the environment type ('rstudio', 'bash', or 'R'). Default is 'rstudio'."
    echo "  -p port       Specify the port number. Default is 8787."
    echo "  -w password   Specify the RStudio password. Default is 'bioc'."
    echo "  -d dockerhome Specify the Docker home directory. Default is '$HOME/dockerhome'."
    echo "  -l            List all available Bioconductor Docker versions."
    echo "  -h            Show this help message."
    echo ""
    echo "The \$DOCKER_RPKGS environment variable is optional and used to specify the R packages directory on the host machine."
    echo "If not set, the default is '\$HOME/.docker-\$version-packages'."
    echo "This directory is mounted into the Docker container at /usr/local/lib/R/host-site-library."
    echo "This allows R packages installed in the container to be persisted on the host machine and shared across multiple containers or sessions."
}

list_versions() {
    echo "Fetching available versions from Docker Hub..."
    curl -s https://registry.hub.docker.com/v2/repositories/bioconductor/bioconductor_docker/tags?page_size=100 | jq -r '.results[].name'
}

version=""
envtype="rstudio"
port=8787
password="bioc"
DOCKER_HOME="$HOME/dockerhome"

while getopts ":v:e:p:w:d:lh" opt; do
    case ${opt} in
        v )
            version=$OPTARG
            ;;
        e )
            envtype=$OPTARG
            ;;
        p )
            port=$OPTARG
            ;;
        w )
            password=$OPTARG
            ;;
        d )
            DOCKER_HOME=$OPTARG
            ;;
        l )
            list_versions
            exit 0
            ;;
        h )
            show_help
            exit 0
            ;;
        \? )
            show_help
            exit 1
            ;;
    esac
done

if [ -z "$version" ]; then
    echo "Error: Version is required. Use the '-v' flag to specify a version. Use the '-l' flag to list available versions or the '-h' flag for examples."
    exit 1
fi

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

biocdocker=bioconductor/bioconductor_docker:"$version"
docker pull $biocdocker
DOCKER_RPKGS="$HOME/.docker-$version-packages"
R_LIBS='/usr/local/lib/R/host-site-library:/usr/local/lib/R/site-library:/usr/local/lib/R/library'
mkdir -p "$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 ""
echo "=================================================="
echo "Installed packages will go in host directory: $DOCKER_RPKGS"
echo "RStudio home directory will be mounted on host directory: $DOCKER_HOME"
echo "=================================================="
echo ""

if [ "$envtype" == "rstudio" ]; then
    echo "=================================================="
    echo "Open RStudio running Bioconductor version $version at http://localhost:$port"
    echo "Login with username: rstudio and password: $password"
    echo "=================================================="
    docker run -e PASSWORD=$password \
        -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 \
        $biocdocker bash
elif [ "$envtype" == "R" ]; 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 R
fi