get rid of old cvmfs2 premount setup

singularity/wrapper_genpipes/bin/container_wrapper.sh

@@ -1,74 +1,29 @@
 #!/bin/bash
 
-
+# Do not modify this file modify ${SCRIPTPATH}/etc/wrapper.conf instead!
 SCRIPTPATH="$( cd "$(dirname "$0")" ; pwd -P )"
 SCRIPTPATH=${SCRIPTPATH%%bin}
 SCRIPTPATH=${SCRIPTPATH%%/}
+GEN_SHARED_CVMFS=/tmp/cvmfs-cache
 
 source ${SCRIPTPATH}/etc/wrapper.conf
-TMPDIR=${TMPDIR:-/tmp}
-
-export GEN_LOCAL_CVMFS=$(mktemp -d $TMPDIR/cvmfs_XXXXX)
-
-GEN_REF=${GEN_LOCAL_CVMFS}/mnt/ref.mugqic
-GEN_SOFT=${GEN_LOCAL_CVMFS}/mnt/soft.mugqic
-
-mkdir -p ${GEN_SOFT}
-mkdir -p ${GEN_REF}
-
-chmod 777 ${GEN_SOFT} ${GEN_REF}
-
-cleaup () {
-#  echo unmounting ${GEN_LOCAL_CVMFS}/mnt
-
-  try=0
-  while  true ; do
-    fusermount -u ${GEN_REF} 2>/dev/null
-    ret=$?
-    if [[ ${ret} -eq 0 || ${try} -ge  ${UMOUNT_RETRY} ]]; then
-      break
-    fi
-    try=$(($try+1))
-    sleep 1
-  done
-
-  while  true ; do
-    fusermount -u ${GEN_SOFT} 2>/dev/null
-    ret=$?
-    if [[ ${ret} -eq 0 || ${try} -ge  ${UMOUNT_RETRY} ]]; then
-      break
-    fi
-    try=$(($try+1))
-    sleep 1
-  done
-
-  rm -r ${GEN_LOCAL_CVMFS}  2>/dev/null
-}
-
-#trap cleaup EXIT
-
-export CVMFS_KEYS_DIR=${SCRIPTPATH}/etc/keys/gen
-export CVMFS_ALIEN_CACHE=${GEN_SHARED_CVMFS}/alien_cache/soft.mugqic
-mkdir -p $CVMFS_ALIEN_CACHE
-chmod 777 $CVMFS_ALIEN_CACHE
-chmod 777 ${GEN_SHARED_CVMFS}/alien_cache
-cvmfs2 -o config=${SCRIPTPATH}/etc/genconfig.conf -o libfuse=3   soft.mugqic \
-${GEN_SOFT}  
-
-export CVMFS_ALIEN_CACHE=${GEN_SHARED_CVMFS}/alien_cache/ref.mugqic
-mkdir -p $CVMFS_ALIEN_CACHE
-chmod 777 $CVMFS_ALIEN_CACHE
-cvmfs2 -o config=${SCRIPTPATH}/etc/genconfig.conf  -o libfuse=3   ref.mugqic \
-${GEN_REF} 
-
-
-#if [ -z ${BIND_LIST+x} ]; then
-#  singularity run --cleanenv -B ${GEN_LOCAL_CVMFS}/mnt:/cvmfs  \
-#  ${SCRIPTPATH}/images/genpipes.sif \
-#  "$@"
-#else
-#  singularity run --cleanenv -B ${GEN_LOCAL_CVMFS}/mnt:/cvmfs  -B "$BIND_LIST" \
-#  ${SCRIPTPATH}/images/genpipes.sif \
-#  "$@"
 
-#fi
+mkdir -p ${GEN_SHARED_CVMFS}
+
+
+if [ -z ${BIND_LIST+x} ]; then
+  singularity run --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 ${GEN_SHARED_CVMFS}:/cvmfs-cache \
+    -B "$BIND_LIST" \
+    --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" \
+    ${SCRIPTPATH}/images/genpipes.sif "$@"
+fi

singularity/wrapper_genpipes/etc/wrapper.conf

@@ -1,5 +1,3 @@
 # GEN_SHARED_CVMFS should have a sufficient amount of space to load full reference files
 export GEN_SHARED_CVMFS=$HOME/cvmfs
-TMPDIR=/tmp
-export UMOUNT_RETRY=5
 BIND_LIST=