Marius,
Thanks for the help with this!
Below is what I am seeing in the logs but it only gets as far as saying the job is queued (the status of the job doesn’t change, even
though torque actually finishes the job successfully-I have something configured wrong):
Dispatching to pbs runner
galaxy.jobs DEBUG 2018-06-14 11:12:22,356 [p:63562,w:2,m:0] [JobHandlerQueue.monitor_thread] (16117) Persisting
job destination (destination id: pbs_default)
galaxy.tools.deps DEBUG 2018-06-14 11:12:22,775 [p:63562,w:2,m:0] [PBSRunner.work_thread-1] Using dependency htseq
version 0.9.1 of type conda
galaxy.tools.deps DEBUG 2018-06-14 11:12:22,775 [p:63562,w:2,m:0] [PBSRunner.work_thread-1] Using dependency samtools
version 1.7 of type conda
galaxy.jobs.command_factory INFO 2018-06-14 11:12:22,857 [p:63562,w:2,m:0] [PBSRunner.work_thread-1] Built script
[/BigData/galaxy/galaxy-dist/database/jobs_directory/016/16117/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/BigData/galaxy/galaxy-dist/conda_deps/envs/mulled-v1-c9f488ec0e9a96bed61dcc2e074b26ce37ed596751861ff368fd824a2a5f11d4" ] ||
galaxy.jobs.runners DEBUG 2018-06-14 11:12:23,143 [p:63562,w:2,m:0] [PBSRunner.work_thread-1] (16117) command is:
rm -rf working; mkdir -p working; cd working; /BigData/galaxy/galaxy-dist/database/jobs_directory/016/16117/tool_script.sh; return_code=$?; cd '/BigData/galaxy/galaxy-dist/database/jobs_directory/016/16117';
galaxy.jobs.runners.pbs DEBUG 2018-06-14 11:12:23,208 [p:63562,w:2,m:0] [PBSRunner.work_thread-1] (16117) submitting
file /BigData/galaxy/galaxy-dist/database/pbs/16117.sh
galaxy.jobs.runners.pbs DEBUG 2018-06-14 11:12:23,214 [p:63562,w:2,m:0] [PBSRunner.work_thread-1] (16117) queued
in default queue as 1434.locahost
galaxy.jobs DEBUG 2018-06-14 11:12:23,214 [p:63562,w:2,m:0] [PBSRunner.work_thread-1] (16117) Persisting job destination (destination id: pbs_default)
From: Marius van den Beek [mailto:m.vandenbeek@gmail.com]
Sent: Thursday, June 14, 2018 6:29 AM
To: Briand, Sheldon (NRC/CNRC) <sheldon.briand@canada.ca>
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] pbs/torque jobs
So I was able to simulate a torque environment with https://github.com/aiidateam/torquessh_base-docker
and that seemed to have worked fine.
I did have to install the torque headers, activate galaxy's virtualenv and install https://github.com/ehiggs/pbs-python.
You should be seeing something like:
```
galaxy.jobs.runners.pbs DEBUG 2018-06-14 09:23:31,549 [p:1944,w:1,m:0] [PBSRunner.work_thread-2] (2) submitting file /home/app/galaxy/database/pbs/2.sh
galaxy.jobs.runners.pbs DEBUG 2018-06-14 09:23:31,551 [p:1944,w:1,m:0] [PBSRunner.work_thread-2] (2) queued in default queue as 3.605046c8289c
galaxy.jobs DEBUG 2018-06-14 09:23:31,552 [p:1944,w:1,m:0] [PBSRunner.work_thread-2] (2) Persisting job destination (destination id: local)
galaxy.jobs.runners.pbs DEBUG 2018-06-14 09:23:31,855 [p:1944,w:1,m:0] [Dummy-5] (2/3.605046c8289c) PBS job state changed from N to R
galaxy.jobs.runners.pbs DEBUG 2018-06-14 09:23:33,994 [p:1944,w:1,m:0] [Dummy-5] (2/3.605046c8289c) PBS job has left queue
galaxy.model.metadata DEBUG 2018-06-14 09:23:34,110 [p:1944,w:1,m:0] [PBSRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 2
galaxy.jobs INFO 2018-06-14 09:23:34,218 [p:1944,w:1,m:0] [PBSRunner.work_thread-3] Collecting metrics for Job 2
galaxy.jobs DEBUG 2018-06-14 09:23:34,234 [p:1944,w:1,m:0] [PBSRunner.work_thread-3] job 2 ended (finish() executed in (189.200 ms))
```
in your logs.
Let me know how this goes.
Best,
Marius
On 14 June 2018 at 10:15, Marius van den Beek <m.vandenbeek@gmail.com> wrote: