From f247bf85b36ca38e820bfc066f36ac64c3ec9d5c Mon Sep 17 00:00:00 2001
From: Matthijs van der Wild <matthijs.van-der-wild@durham.ac.uk>
Date: Wed, 9 Apr 2025 16:27:03 +0100
Subject: use a single assignment of possibly pre-set APPTAINER variables

---
 pilot.sh | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

(limited to 'pilot.sh')

diff --git a/pilot.sh b/pilot.sh
index 8b9e048..736f9a2 100644
--- a/pilot.sh
+++ b/pilot.sh
@@ -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
-- 
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