Thanks for the bug report, that is indeed a problem - I am not sure
how the torque runner here would ever reach a complete job state. I
prefer the following fix however, if you would be willing to verify it
fixes the problem you are encountering I would be happy to apply it to
Galaxy's stable branch.
diff -r 6a633b37c4c4 lib/galaxy/jobs/runners/cli_job/torque.py
--- a/lib/galaxy/jobs/runners/cli_job/torque.py Fri Feb 28 08:52:52 2014 -0500
+++ b/lib/galaxy/jobs/runners/cli_job/torque.py Fri Feb 28 08:32:41 2014 -0600
@@ -131,4 +131,5 @@
def __get_job_state(self, state):
return { 'E' : job_states.RUNNING,
'R' : job_states.RUNNING,
- 'Q' : job_states.QUEUED }.get(state, state)
+ 'Q' : job_states.QUEUED,
+ 'C' : job_states.OK }.get(state, state)
-John
On Fri, Feb 28, 2014 at 12:13 AM, ngsf...@hygenomics.com
<ngsf...@hygenomics.com> wrote:
> Hi,
>
> base:
> os:centos6.4
> torque:4.2.7
>
> I built a glaxy cluster today,and then I found the job completion status of
> torque queue is 'c',but the need state of galalxy is "ok".So I modified the
> torque.py file and solved this error. I do, right?
>
>
> diff -r 8411a9f30feb lib/galaxy/jobs/runners/cli_job/torque.py
> --- a/lib/galaxy/jobs/runners/cli_job/torque.py Thu Dec 19 14:38:03 2013
> -0500
> +++ b/lib/galaxy/jobs/runners/cli_job/torque.py Fri Feb 28 13:02:48 2014
> +0800
> @@ -117,6 +117,8 @@
> if id in job_ids:
> state = job.find('job_state').text
> # map PBS job states to Galaxy job states.
> + if state == u'C' :
> + state = 'ok'
> rval[id] = self.__get_job_state(state)
> return rval
>
> ________________________________
> ngsf...@hygenomics.com
>
> ___________________________________________________________
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