Update script to run on cluster or pisa.

singularity/workflows_shell.sh

@@ -49,7 +49,7 @@ then
     module --version 2> /dev/null && have_modules=1
     if [ ${have_modules} ]
     then
-        module load singularity || error_exit "singularity is needed to run the pipelines (see ${install_doc})"
+        module load apptainer || error_exit "singularity is needed to run the pipelines (see ${install_doc})"
     else
         error_exit "singularity is needed to run the pipelines (see ${install_doc})"
     fi
@@ -77,6 +77,6 @@ case ${1} in
         # -B /pasteur will mount /pasteur in the container
         # so that it finds the Genome configuration and gene lists
         # that are expected to be in a specific location there.
-        singularity shell -B /pasteur -B /run/shm:/run/shm ${container} $@
+        [[ $(hostname) = "pisa" ]] && SINGULARITYENV_USER=${USER} singularity shell -B /pasteur -B /run/shm:/run/shm ${container} $@ || APPTAINERENV_USER=${USER} apptainer shell -B /opt/hpc/slurm -B /var/run/munge -B /pasteur ${container} $@
         ;;
 esac