diff --git a/singularity/workflows_shell.sh b/singularity/workflows_shell.sh index db220eaf7d394c46cb81dc126b91580bd7e13d99..267ef30cac84341995c408ff8c529fe3d50ef1b6 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