Need to set default HOME/TMP before env_setup_commands

Otherwise the defaults take precedence
galaxyproject · Jun 10, 2018 · 77cd1fc · 77cd1fc
1 parent bbce9a1
commit 77cd1fc
Showing 1 changed file with 2 additions and 2 deletions.
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
@@ -4,6 +4,8 @@ $headers
 
 _galaxy_setup_environment() {
     local _use_framework_galaxy="$1"
+    _GALAXY_JOB_HOME_DIR="$working_directory/home"
+    _GALAXY_JOB_TMP_DIR=$tmp_dir_creation_statement
     $env_setup_commands
     if [ "$GALAXY_LIB" != "None" -a "$_use_framework_galaxy" = "True" ]; then
         if [ -n "$PYTHONPATH" ]; then
@@ -13,8 +15,6 @@ _galaxy_setup_environment() {
         fi
         export PYTHONPATH
     fi
-    _GALAXY_JOB_HOME_DIR="$working_directory/home"
-    _GALAXY_JOB_TMP_DIR=$tmp_dir_creation_statement
     # These don't get cleaned on a re-run but may in the future.
     [ -z "$_GALAXY_JOB_TMP_DIR" -a ! -f "$_GALAXY_JOB_TMP_DIR" ] || mkdir -p "$_GALAXY_JOB_TMP_DIR"
     [ -z "$_GALAXY_JOB_HOME_DIR" -a ! -f "$_GALAXY_JOB_HOME_DIR" ] || mkdir -p "$_GALAXY_JOB_HOME_DIR"