I'm not sure what the issue could be, the PBS runner hasn't been updated in
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 ?
When you are submitting a job in galaxy what messages are you seeing in the
On 13 June 2018 at 22:07, Briand, Sheldon (NRC/CNRC) <
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.
*From:* Marius van den Beek [mailto:firstname.lastname@example.org]
*Sent:* Wednesday, June 13, 2018 4:58 PM
*To:* Briand, Sheldon (NRC/CNRC) <sheldon.briand(a)canada.ca>
*Subject:* Re: [galaxy-dev] pbs/torque jobs
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 ?
On 13 June 2018 at 21:13, Briand, Sheldon (NRC/CNRC) <
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?
Computer Systems and Applications Analyst
National Research Council/Government of Canada
Sheldon.briand(a)canada.ca/ Tel: (902) 426-1677
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