From bed931ad81ae3821a6b7f4e8e2f09003f5c12012 Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Tue, 19 Apr 2016 18:57:23 +0200
Subject: [PATCH] Sync job script templates with galaxy
---
pulsar/managers/util/job_script/CLUSTER_SLOTS_STATEMENT.sh | 2 ++
pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh | 3 ++-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/pulsar/managers/util/job_script/CLUSTER_SLOTS_STATEMENT.sh b/pulsar/managers/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
index 3e59bbd0..624f77c4 100644
--- a/pulsar/managers/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
+++ b/pulsar/managers/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
@@ -15,6 +15,8 @@ elif [ -n "$SLURM_NTASKS" ] || [ -n "$SLURM_CPUS_PER_TASK" ]; then
GALAXY_SLOTS=`expr "${SLURM_NTASKS:-1}" \* "${SLURM_CPUS_PER_TASK:-1}"`
elif [ -n "$NSLOTS" ]; then
GALAXY_SLOTS="$NSLOTS"
+elif [ -n "$NCPUS" ]; then
+ GALAXY_SLOTS="$NCPUS"
elif [ -n "$PBS_NCPUS" ]; then
GALAXY_SLOTS="$PBS_NCPUS"
elif [ -f "$PBS_NODEFILE" ]; then
diff --git a/pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh b/pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
index 0c533ce0..6b3c283b 100644
--- a/pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
+++ b/pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
@@ -1,6 +1,7 @@
#!$shell
-$integrity_injection
+
$headers
+$integrity_injection
$slots_statement
export GALAXY_SLOTS
GALAXY_LIB="$galaxy_lib"
--
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