From 3d35e6eb50522fb9e80957fd4610046d8ed7cc7f Mon Sep 17 00:00:00 2001 From: P-O Quirion Date: Thu, 12 Aug 2021 15:20:10 -0400 Subject: [PATCH] add genpipes envfile for container --- singularity/wrapper_genpipes/bin/container_wrapper.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/singularity/wrapper_genpipes/bin/container_wrapper.sh b/singularity/wrapper_genpipes/bin/container_wrapper.sh index 10e8a6e..45158e5 100755 --- a/singularity/wrapper_genpipes/bin/container_wrapper.sh +++ b/singularity/wrapper_genpipes/bin/container_wrapper.sh @@ -12,14 +12,14 @@ mkdir -p ${GEN_SHARED_CVMFS} if [ -z ${BIND_LIST+x} ]; then - singularity run --cleanenv -S /var/run/cvmfs -B ${GEN_SHARED_CVMFS}:/cvmfs-cache \ + singularity run --env-file $HOME/.genpipes_env --cleanenv -S /var/run/cvmfs -B ${GEN_SHARED_CVMFS}:/cvmfs-cache \ --fusemount \ "container:cvmfs2 cvmfs-config.computecanada.ca /cvmfs/cvmfs-config.computecanada.ca" \ --fusemount "container:cvmfs2 soft.mugqic /cvmfs/soft.mugqic" \ --fusemount "container:cvmfs2 ref.mugqic /cvmfs/ref.mugqic" \ ${SCRIPTPATH}/images/genpipes.sif "$@" else - singularity run --cleanenv -S /var/run/cvmfs -B ${GEN_SHARED_CVMFS}:/cvmfs-cache \ + singularity run --env-file $HOME/.genpipes_env --cleanenv -S /var/run/cvmfs -B ${GEN_SHARED_CVMFS}:/cvmfs-cache \ -B "$BIND_LIST" \ --fusemount \ "container:cvmfs2 cvmfs-config.computecanada.ca /cvmfs/cvmfs-config.computecanada.ca" \