From 7bf6683baad48d714f6fabb2775d5f6973d2cb5d Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 10 Jul 2024 12:53:37 +0200
Subject: [PATCH] Update script to run on cluster or pisa.
---
singularity/workflows_shell.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/singularity/workflows_shell.sh b/singularity/workflows_shell.sh
index db220ea..267ef30 100755
--- a/singularity/workflows_shell.sh
+++ b/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
--
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