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Commit 7bf6683b authored by Blaise Li's avatar Blaise Li
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Update script to run on cluster or pisa.

parent 43ec501e
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...@@ -49,7 +49,7 @@ then ...@@ -49,7 +49,7 @@ then
module --version 2> /dev/null && have_modules=1 module --version 2> /dev/null && have_modules=1
if [ ${have_modules} ] if [ ${have_modules} ]
then 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 else
error_exit "singularity is needed to run the pipelines (see ${install_doc})" error_exit "singularity is needed to run the pipelines (see ${install_doc})"
fi fi
...@@ -77,6 +77,6 @@ case ${1} in ...@@ -77,6 +77,6 @@ case ${1} in
# -B /pasteur will mount /pasteur in the container # -B /pasteur will mount /pasteur in the container
# so that it finds the Genome configuration and gene lists # so that it finds the Genome configuration and gene lists
# that are expected to be in a specific location there. # 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 esac
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