moved assign_all_groups parameter to config

config/galaxy.ini.sample

@@ -1306,7 +1306,7 @@ use_interactive = True
 #
 # https://galaxyproject.org/admin/config/performance/cluster
 #
-#drmaa_external_runjob_script = sudo -E scripts/drmaa_external_runner.py
+#drmaa_external_runjob_script = sudo -E scripts/drmaa_external_runner.py --assign_all_groups
 #drmaa_external_killjob_script = sudo -E scripts/drmaa_external_killer.py
 #external_chown_script = sudo -E scripts/external_chown_script.py
 

lib/galaxy/jobs/runners/drmaa.py

@@ -364,7 +364,6 @@ class DRMAAJobRunner( AsynchronousJobRunner ):
         """
         command = shlex.split( external_runjob_script )
         command.extend( [ str(username), jobtemplate_filename ] )
-        command.append( "--assign_all_groups"  )
         log.info("Running command %s" % command)
         p = subprocess.Popen(command,
                              shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)

scripts/drmaa_external_runner.py

@@ -84,7 +84,8 @@ def validate_paramters():
 
 def set_user(uid, assign_all_groups):
     try:
-        # Get user's default group and set it to current process to make sure file permissions are inherited correctly
+        # Get user's default group and set it to current process to make sure
+        # file permissions are inherited correctly
         # Solves issue with permission denied for JSON files
         gid = pwd.getpwuid(uid).pw_gid
         import grp