Hi Sheldon, I'm not sure what the issue could be, the PBS runner hasn't been updated in ~3 years, but of course many things around it have been. Could you set galaxy's logging level to debug if it isn't already and check the logs ? ( https://github.com/galaxyproject/galaxy/blob/release_18.05/config/galaxy.yml.sample#L895 ) When you are submitting a job in galaxy what messages are you seeing in the logs ?
Best, Marius On 13 June 2018 at 22:07, Briand, Sheldon (NRC/CNRC) < [email protected]> wrote: > Hi Marius, > > > > The PBS runner and the user is the galaxy user. I do not use the run as > real user option. I haven’t been using drmaa_external_runjob_script. > This setup worked for my old 17.05 and previous versions of galaxy. > > > > Thanks, > > -Sheldon > > > > *From:* Marius van den Beek [mailto:[email protected]] > *Sent:* Wednesday, June 13, 2018 4:58 PM > *To:* Briand, Sheldon (NRC/CNRC) <[email protected]> > *Cc:* [email protected] > *Subject:* Re: [galaxy-dev] pbs/torque jobs > > > > Hi Sheldon, > > > > is there anything particular about your job configuration, e.g. > > are you you using the run as real user option or are you using > > the drmaa_external_runjob_script option ? > > Are you using the drmaa or the PBS runner ? > > > > Best, > > Marius > > > > On 13 June 2018 at 21:13, Briand, Sheldon (NRC/CNRC) < > [email protected]> wrote: > > Hi, > > > > I have upgraded to Galaxy 18.05 (from 17.05). I am running a torque job > scheduler (version 6.02). > > > > When I submit a job through galaxy and I look in the admin/manage jobs > section I see that the job has been submitted successfully. It shows that > the job is queued and waiting to run. On the cluster I see that the job > runs and goes to completion. However, the status in galaxy continue to > show that the job is waiting to run and the status never gets updated. I’m > using postgres as my database and I am running through a nginx proxy. > > > > I see no errors in my galaxy.log file. > > > > I switched from galaxy.ini to galaxy.yml and from paste to uwsgi. Is this > a configuration problem on my end? Where should I be looking? > > > > Thanks, > > -Sheldon > > > > Sheldon Briand > > Computer Systems and Applications Analyst > > National Research Council/Government of Canada > > [email protected]/ Tel: (902) 426-1677 > > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > > >
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