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

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

module load mugqic/genpipes${PIPELINE_VERSION}