stdout and stderr files
Hi, I have a personal galaxy instance with the runner as SGE. I am able to successfully submit jobs, and the output folder is created at $file_path. But I see that the SGE job log files ie., stdout and stderr - <job-name>.o and <job-name>.e are being removed in the cleanup function in sge.py. Is this right? Is galaxy capturing the jobs stdout and stderr some where else? Also when I click on the link “Tool Standard Output” from galaxy web interface, it returns empty. Is there a setting that I should have to view jobs stdout, stderr from the web interface? Thanks, Poornima.
Yes, Galaxy stores the stdout and stderr in the database once the job is complete. The .o and .e files are automatically removed once this is complete. You should be able to click on the tool panel's (the panel on the righthand side) info button for each tool, which is what it appears you are doing. There shouldn't be anything that you have to set to see the stdout and stderr. Are you able to see output for other tools? -Scott ----- Original Message -----
Hi,
I have a personal galaxy instance with the runner as SGE. I am able to successfully submit jobs, and the output folder is created at $file_path. But I see that the SGE job log files ie., stdout and stderr - <job-name>.o and <job-name>.e are being removed in the cleanup function in sge.py. Is this right? Is galaxy capturing the jobs stdout and stderr some where else?
Also when I click on the link “Tool Standard Output” from galaxy web interface, it returns empty. Is there a setting that I should have to view jobs stdout, stderr from the web interface?
Thanks, Poornima. ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
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Thanks Scott. I did find them in the database in the table “job”. So far, the jobs that I ran - FastQ formatting and QA did not produce any stdout and stderr and thats why I couldn’t see any content by clicking on the info button, and database table also shows empty rows. I ran a FastQ trimmer job, which did produce stdout and I was able to see this from galaxy web interface by clicking on “Tool Standard Output” link and also in the database table. Another suggestion I got from local galaxy-dev was that, by enabling debugging (set "debug = True" in universe_wsgi.ini) .o and .e files are preserved in the $file_path and are not removed once the job is complete. Thanks, Poornima. On Jun 11, 2012, at 11:18 AM, Scott McManus wrote:
Yes, Galaxy stores the stdout and stderr in the database once the job is complete. The .o and .e files are automatically removed once this is complete.
You should be able to click on the tool panel's (the panel on the righthand side) info button for each tool, which is what it appears you are doing. There shouldn't be anything that you have to set to see the stdout and stderr. Are you able to see output for other tools?
-Scott
----- Original Message -----
Hi,
I have a personal galaxy instance with the runner as SGE. I am able to successfully submit jobs, and the output folder is created at $file_path. But I see that the SGE job log files ie., stdout and stderr - <job-name>.o and <job-name>.e are being removed in the cleanup function in sge.py. Is this right? Is galaxy capturing the jobs stdout and stderr some where else?
Also when I click on the link “Tool Standard Output” from galaxy web interface, it returns empty. Is there a setting that I should have to view jobs stdout, stderr from the web interface?
Thanks, Poornima. ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
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Poornima Pochana -
Scott McManus