yes, i think galaxy already grabs these files.  i seem to recall this process would get stuck if the output was too large (i was running something with a --debug/verbose option and galaxy would not finish the job even though it was off the cluster -- had to redirect to a log file).

so i guess others aren't having the same problems as i had, which is good news

On Thu, Dec 1, 2011 at 10:01 AM, Nate Coraor <nate@bx.psu.edu> wrote:

On Nov 29, 2011, at 9:22 PM, Fields, Christopher J wrote:

> On Nov 29, 2011, at 3:13 AM, Peter Cock wrote:
>
>> On Monday, November 28, 2011, Joseph Hargitai <joseph.hargitai@einstein.yu.edu> wrote:
>>> Ed,
>>>
>>> we had the classic goof on our cluster with this. 4 nodes could not see the /home/galaxy folder due to a missing entry in /etc/fstab. When the jobs hit those nodes (which explains the randomness) we got the error message.
>>>
>>> Bothersome was the lack of good logs to go on. The error message was too generic - however I discovered that Galaxy was depositing the error and our messages in the /pbs folder and you could briefly read them before they got deleted. There the message was the classic SGE input/output message - /home/galaxy.... file not found.
>>>
>>> Hence my follow up question - how can I have galaxy NOT to delete these SGE error and out files?
>>>
>>> best,
>>> joe
>>
>> Better yet, Galaxy should read the SGE o and e files and record their contents as it would for a directly executed tools stdout and stderr.
>>
>> Peter
>
> ...or at least have the option to do so, maybe a level of verbosity.  I have been bitten by lack of stderr output myself, where having it might have saved some manual debugging.

Unless I'm misunderstanding, this is what Galaxy already does.  stdout/stderr up to 32K are read from .o and .e and stored in job.stdout/job.stderr.  We do need to just store them as files and make them accessible for each tool run, this will hopefully happen sometime soonish.

--nate

>
> chris
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