diff options
| author | Matthijs van der Wild <matthijs.van-der-wild@durham.ac.uk> | 2025-04-09 16:27:03 +0100 |
|---|---|---|
| committer | Matthijs van der Wild <matthijs.van-der-wild@durham.ac.uk> | 2025-04-09 16:27:03 +0100 |
| commit | f247bf85b36ca38e820bfc066f36ac64c3ec9d5c (patch) | |
| tree | 2716e808727cd2051c464a7ea9774c37fe6cbb05 | |
| parent | 398f330c873563b2ab44bc01b0b9fedf3de8f061 (diff) | |
use a single assignment of possibly pre-set APPTAINER variables
| -rw-r--r-- | pilot.sh | 25 |
1 files changed, 12 insertions, 13 deletions
@@ -90,11 +90,6 @@ Intermediate output directory ┃ ${TMP_OUTDIR} Pipeline statistics directory ┃ ${STATS_DIR} EOF -# TODO: set dummy variables that potentially use pre-set values -export APPTAINERENV_PATH="\$PATH:$PIPELINE/scripts" -export APPTAINERENV_PYTHONPATH="\$PYTHONPATH:$PIPELINE/scripts" -export APPTAINER_BIND="$HOME,$INPUT_DIR,$OUTPUT_DIR" - TOIL_COMMAND="toil-cwl-runner ${RESTART} ${TMPDIR_PREFIX} \ --singularity \ --clean never \ @@ -122,16 +117,20 @@ export TOIL_SLURM_ARGS="${TOIL_SLURM_ARGS:-"-p cosma5 -A durham -t 72:00:00"}" # -A # project # -t # runtime in d-hh:mm:ss format -echo -e "env APPTAINERENV_PREPEND_PATH="$PIPELINE/scripts:\$PATH" \ - APPTAINERENV_PYTHONPATH="$PIPELINE/scripts:\$PYTHONPATH" \ - APPTAINER_BIND="$HOME,$INPUT_DIR,${OUTPUT_DIR}" \ - TOIL_SLURM_ARGS="${TOIL_SLURM_ARGS:-"-p cosma5 -A durham -t 72:00:00"}" \ +export APPTAINERENV_PREPEND_PATH=${APPTAINERENV_PREPEND_PATH:-"$PIPELINE/scripts"} +export APPTAINERENV_PYTHONPATH=${APPTAINERENV_PYTHONPATH:-"$PIPELINE/scripts:\$PYTHONPATH"} +export APPTAINER_BIND=${APPTAINER_BIND:-"$HOME,$INPUT_DIR,$OUTPUT_DIR"} + +echo -e "env APPTAINERENV_PREPEND_PATH="$APPTAINERENV_PREPEND_PATH" \ + APPTAINERENV_PYTHONPATH="$APPTAINERENV_PYTHONPATH" \ + APPTAINER_BIND="$APPTAINER_BIND" \ + TOIL_SLURM_ARGS="$TOIL_SLURM_ARGS" \ ${TOIL_COMMAND}" -env APPTAINERENV_PREPEND_PATH="$PIPELINE/scripts" \ - APPTAINERENV_PYTHONPATH="$PIPELINE/scripts:\$PYTHONPATH" \ - APPTAINER_BIND="$HOME,$INPUT_DIR,$OUTPUT_DIR" \ - TOIL_SLURM_ARGS="${TOIL_SLURM_ARGS:--p cosma5 -A durham -t 72:00:00}" \ +env APPTAINERENV_PREPEND_PATH="$APPTAINERENV_PREPEND_PATH" \ + APPTAINERENV_PYTHONPATH="$APPTAINERENV_PYTHONPATH" \ + APPTAINER_BIND="$APPTAINER_BIND" \ + TOIL_SLURM_ARGS="$TOIL_SLURM_ARGS" \ ${TOIL_COMMAND} > ${OUTPUT_DIR}/${WORKFLOW_NAME}.out && STATUS=${?} || STATUS=${?} toil stats --raw ${JOBSTORE_DIR} > ${STATS_DIR}/${WORKFLOW_NAME}.stats.json || true |