diff options
| -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}" \ |