diff options
| author | Matthijs van der Wild <matthijs.van-der-wild@durham.ac.uk> | 2025-04-07 09:51:38 +0100 |
|---|---|---|
| committer | Matthijs van der Wild <matthijs.van-der-wild@durham.ac.uk> | 2025-04-07 09:51:38 +0100 |
| commit | 398f330c873563b2ab44bc01b0b9fedf3de8f061 (patch) | |
| tree | 7cbea68390de871811da44dd1eebf5e6018c4359 /pilot.sh | |
| parent | 5cbd46d2c6260bb8fe60ef0d779eb024ae10f849 (diff) | |
append to container PATH through APPTAINERENV_PREPEND_PATH
Apptainer v1.3.6-1.el9 doesn't appear to allow resetting the
container path using APPTAINERENV_PATH. Using this variable
works in v1.3.4, but it isn't clear where this change was
introduced. APPTAINERENV_PREPEND_PATH is a safe alternative.
Diffstat (limited to 'pilot.sh')
| -rw-r--r-- | pilot.sh | 4 |
1 files changed, 2 insertions, 2 deletions
@@ -122,13 +122,13 @@ export TOIL_SLURM_ARGS="${TOIL_SLURM_ARGS:-"-p cosma5 -A durham -t 72:00:00"}" # -A # project # -t # runtime in d-hh:mm:ss format -echo -e "env APPTAINERENV_PATH="$PIPELINE/scripts:\$PATH" \ +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"}" \ ${TOIL_COMMAND}" -env APPTAINERENV_PATH="$PIPELINE/scripts:\$PATH" \ +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}" \ |