From 53078b42afe3e162665e885b51249320b449edd8 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 19 Sep 2017 13:44:23 -0400
Subject: [PATCH] Job script template from Galaxy
---
.../managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
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 2a83d133..68da1b3e 100644
--- a/pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
+++ b/pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
@@ -1,5 +1,7 @@
#!$shell
+$headers
+
_galaxy_setup_environment() {
local _use_framework_galaxy="$1"
if [ "$GALAXY_LIB" != "None" -a "$_use_framework_galaxy" = "True" ]; then
@@ -11,18 +13,17 @@ _galaxy_setup_environment() {
export PYTHONPATH
fi
$env_setup_commands
- if [ "$GALAXY_VIRTUAL_ENV" != "None" -a "$_use_framework_galaxy" = "True" \
- -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" \
+ if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" \
-a "`command -v python`" != "$GALAXY_VIRTUAL_ENV/bin/python" ]; then
. "$GALAXY_VIRTUAL_ENV/bin/activate"
fi
}
-$headers
$integrity_injection
$slots_statement
export GALAXY_SLOTS
GALAXY_VIRTUAL_ENV="$galaxy_virtual_env"
+_GALAXY_VIRTUAL_ENV="$galaxy_virtual_env"
PRESERVE_GALAXY_ENVIRONMENT="$preserve_python_environment"
GALAXY_LIB="$galaxy_lib"
_galaxy_setup_environment "$PRESERVE_GALAXY_ENVIRONMENT"
--
GitLab