From 1954aff199dba540be602e72b9c64068c1359950 Mon Sep 17 00:00:00 2001
From: Matthijs van der Wild <matthijs.van-der-wild@durham.ac.uk>
Date: Mon, 31 Mar 2025 23:55:08 +0100
Subject: place script directory at head of (PYTHON)PATH

---
 pilot.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'pilot.sh')

diff --git a/pilot.sh b/pilot.sh
index 0131b02..2ecef80 100644
--- a/pilot.sh
+++ b/pilot.sh
@@ -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=${?} || STATUS=${?}
-- 
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