Job script enhancements based on feedback.

galaxyproject · Sep 21, 2017 · 276af4d · 276af4d
1 parent 74ad0ac
commit 276af4d
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py
@@ -17,7 +17,7 @@
 CAPTURE_RETURN_CODE = "return_code=$?"
 YIELD_CAPTURED_CODE = 'sh -c "exit $return_code"'
 SETUP_GALAXY_FOR_METADATA = """
-_galaxy_setup_environment True
+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True
 """
 
 

diff --git a/lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh b/lib/galaxy/jobs/runners/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"