gistfile1.diff

diff -r a973453e1e68 lib/galaxy/jobs/runners/pbs.py
--- a/lib/galaxy/jobs/runners/pbs.py	Fri Nov 15 10:50:49 2013 -0500
+++ b/lib/galaxy/jobs/runners/pbs.py	Fri Nov 15 13:58:42 2013 -0500
@@ -49,7 +49,7 @@
 """

 PBS_ARGMAP = {
-    'destination'           : '-d',
+    'destination'           : '-q',
     'Execution_Time'        : '-a',
     'Account_Name'          : '-A',
     'Checkpoint'            : '-c',
@@ -213,6 +213,8 @@
         pbs_queue_name = None
         pbs_server_name = self.default_pbs_server
         pbs_options = []
+        if '-q' in job_destination.params and 'destination' not in job_destination.params:
+            job_destination.params['destination'] = job_destination.params.pop('-q')
         if 'destination' in job_destination.params:
             if '@' in job_destination.params['destination']:
                 # Destination includes a server