From 398f330c873563b2ab44bc01b0b9fedf3de8f061 Mon Sep 17 00:00:00 2001 From: Matthijs van der Wild Date: Mon, 7 Apr 2025 09:51:38 +0100 Subject: 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. --- pilot.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pilot.sh') diff --git a/pilot.sh b/pilot.sh index c4b16a6..8b9e048 100644 --- a/pilot.sh +++ b/pilot.sh @@ -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}" \ -- cgit v1.2.3