Fix default job script by moving env setup

The part where pythonpath was evaluated totally ignored any variables set in the env setup. That is now fixed. All credits go to @mvdbeek for finding the cause of the issue and proposing the solution.

lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh

@@ -3,6 +3,7 @@
 $headers
 
 _galaxy_setup_environment() {
+    $env_setup_commands
     local _use_framework_galaxy="$1"
     if [ "$GALAXY_LIB" != "None" -a "$_use_framework_galaxy" = "True" ]; then
         if [ -n "$PYTHONPATH" ]; then
@@ -14,7 +15,6 @@ _galaxy_setup_environment() {
     fi
     _GALAXY_JOB_HOME_DIR="$working_directory/home"
     _GALAXY_JOB_TMP_DIR=$tmp_dir_creation_statement
-    $env_setup_commands
     # These don't get cleaned on a re-run but may in the future.
     [ -z "$_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"