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.
>> ___________________________________________________________
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