diff options
| author | Matthijs van der Wild <matthijs.van-der-wild@durham.ac.uk> | 2025-03-31 23:55:08 +0100 |
|---|---|---|
| committer | Matthijs van der Wild <matthijs.van-der-wild@durham.ac.uk> | 2025-03-31 23:55:08 +0100 |
| commit | 1954aff199dba540be602e72b9c64068c1359950 (patch) | |
| tree | 052bb21c02db60748924c0a435a2e2729d0ec069 /pilot.sh | |
| parent | f94ad8a6e9ad29b2821e63211c54bd5b92668807 (diff) | |
place script directory at head of (PYTHON)PATH
Diffstat (limited to 'pilot.sh')
| -rw-r--r-- | pilot.sh | 4 |
1 files changed, 2 insertions, 2 deletions
@@ -127,8 +127,8 @@ echo -e "env APPTAINERENV_PATH="$PIPELINE/scripts:\$PATH" \ TOIL_SLURM_ARGS="${TOIL_SLURM_ARGS:-"-p cosma5 -A durham -t 72:00:00"}" \ ${TOIL_COMMAND}" -env APPTAINERENV_PATH="\$PATH:$PIPELINE/scripts" \ - APPTAINERENV_PYTHONPATH="\$PYTHONPATH:$PIPELINE/scripts" \ +env APPTAINERENV_PATH="$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}" \ ${TOIL_COMMAND} > ${OUTPUT_DIR}/${WORKFLOW_NAME}.out && STATUS=${?} || STATUS=${?} |