genpipesrc

#source /etc/bashrc
#source ~/.bashrc
if [ -z "${QUIET+x}" ]; then
    echo -e "\nWait while Genpipes module are loaded. This could take a while, especially if the cvmfs cache is new.\n"
fi

mount -l | grep soft.mugqic 2>/dev/null 1>&2
retcode=$?
if [ ${retcode} -ne 0 ] ; then
    # should only run in docker container, not singularity
    mount -t cvmfs cvmfs-config.computecanada.ca /cvmfs/cvmfs-config.computecanada.ca/
    mount -t cvmfs ref.mugqic /cvmfs/ref.mugqic
    mount -t cvmfs soft.mugqic /cvmfs/soft.mugqic
fi

module use $MUGQIC_INSTALL_HOME/modulefiles

if [ -z "${GENPIPES_VERSION+x}" ]; then
    GENPIPES_VERSION=$(module avail -d mugqic/genpipes 2>&1 | grep -o '[0-9]\.[0-9]\.[0-9]')
    export GENPIPES_VERSION=${GENPIPES_VERSION}
fi

if [[ ${GENPIPES_VERSION##/} =~ 3\.[0-9]+\.[0-9]+ ]]; then
    # version 3 releases are in python 2
    module load mugqic/python/2.7.14
elif [[ ${GENPIPES_VERSION##/} =~ 4\.[0-9]+\.[0-9]+ ]]; then
    # version 4 releases are in python 3
    module load mugqic/python/3.10.4
else
    # 5 and up are NOT loading python anymore as GenPipes is now a pip package
    :
fi

if [[ ${GENPIPES_VERSION##/} =~ local ]]; then
    # Development mode, using the cloned repo mounted as /genpipes
    if [ -f /genpipes/.genpipes_container_venv/bin/activate ]; then
        module load mugqic/python/3.12.2
        source /genpipes/.genpipes_container_venv/bin/activate
    else
        module load mugqic/python/3.12.2
        python3 -m venv /genpipes/.genpipes_container_venv
        source /genpipes/.genpipes_container_venv/bin/activate
        pip install --prefix=/genpipes/.genpipes_container_venv /genpipes
    fi
else
    # Not in development mode
    module load mugqic/genpipes/${GENPIPES_VERSION}
fi