diff --git a/singularity/run_pipeline.sh b/singularity/run_pipeline.sh index ac4eb56f5f32c28ecd21394c1e23cd119edadd64..ddb47de346cc971e23c8197c67d312cc3398264e 100755 --- a/singularity/run_pipeline.sh +++ b/singularity/run_pipeline.sh @@ -114,7 +114,7 @@ cluster_opts="--cluster \\\'sbatch --mem={cluster.ram} --cpus-per-task={threads} #cluster_opts="--cores 20 --cluster \'sbatch --mem={cluster.ram} --cpus-per-task={threads} --job-name={rule}-{wildcards} --qos=${QOS} --part=${PART} --mpi=none\' -j 300" #cmd="APPTAINERENV_USER=${USER} apptainer run --cleanenv -B /opt/hpc/slurm -B /var/run/munge -B /pasteur ${container} ${PROGNAME} ${pipeline_config} ${cluster_opts} --cluster-config ${cluster_config}" #cmd="APPTAINERENV_USER=${USER} apptainer run --cleanenv -B /opt/hpc/slurm -B /var/run/munge -B /pasteur ${container} ${PROGNAME} $@" -cmd="APPTAINERENV_USER=${USER} apptainer run -B /opt/hpc/slurm -B /var/run/munge -B /pasteur ${container} ${PROGNAME} $@ ${cluster_opts}" +cmd="APPTAINERENV_USER=${USER} apptainer run -B /opt/hpc/slurm -B /var/run/munge -B /pasteur -B /local ${container} ${PROGNAME} $@ ${cluster_opts}" # This script can be called from various symbolic links. # The name of the link determines which snakefile to use. @@ -127,6 +127,6 @@ cmd="APPTAINERENV_USER=${USER} apptainer run -B /opt/hpc/slurm -B /var/run/munge # that are expected to be in a specific location there. # singularity run -B /pasteur -B /run/shm:/run/shm ${container} ${PROGNAME} $@ #[[ $(hostname) = "pisa" ]] && SINGULARITYENV_USER=${USER} singularity run --cleanenv -B /pasteur -B /run/shm:/run/shm ${container} ${PROGNAME} $@ || sbatch --qos=${QOS} --part=${PART} --wrap="${cmd}" -[[ $(hostname) = "pisa" ]] && SINGULARITYENV_USER=${USER} singularity run -B /pasteur -B /run/shm:/run/shm ${container} ${PROGNAME} $@ || sbatch --qos=${QOS} --part=${PART} --wrap="${cmd}" +[[ $(hostname) = "pisa" ]] && SINGULARITYENV_USER=${USER} singularity run -B /pasteur -B /local -B /run/shm:/run/shm ${container} ${PROGNAME} $@ || sbatch --qos=${QOS} --part=${PART} --wrap="${cmd}" exit 0 diff --git a/singularity/workflows_shell.sh b/singularity/workflows_shell.sh index 267ef30cac84341995c408ff8c529fe3d50ef1b6..fcce92b5df630371f8da5ed22e15eb25bb289899 100755 --- a/singularity/workflows_shell.sh +++ b/singularity/workflows_shell.sh @@ -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. - [[ $(hostname) = "pisa" ]] && SINGULARITYENV_USER=${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} $@ + [[ $(hostname) = "pisa" ]] && SINGULARITYENV_USER=${USER} singularity shell -B /pasteur -B /local -B /run/shm:/run/shm ${container} $@ || APPTAINERENV_USER=${USER} apptainer shell -B /opt/hpc/slurm -B /var/run/munge -B /pasteur -B /local ${container} $@ ;; esac diff --git a/singularity/wrap_in_container.sh b/singularity/wrap_in_container.sh index a05a8ed0445ba0baa94a29dfdef3f76d91c42075..cdc23c97c907b65e155c502d582ea616664fdae7 100755 --- a/singularity/wrap_in_container.sh +++ b/singularity/wrap_in_container.sh @@ -71,6 +71,6 @@ fi echo "${PROGNAME} found ${container}" -APPTAINERENV_USER=${USER} apptainer exec -B /pasteur ${container} $@ +APPTAINERENV_USER=${USER} apptainer exec -B /pasteur -B /local ${container} $@ exit 0