On Jul 18, 2012, at 4:17 PM, Anthonius deBoer wrote:

> Hi,
> 
> I am running into some out-of-disk space errors with some of my jobs and this 
> was because the /tmp space is running out of space.
> 
> I want to use a different temporary directory but I can't get GALAXY to pick 
> up my settings...
> 
> I use this in the .ini file
> 
> # Temporary files are stored in this directory.
> new_file_path = /mnt/ngs/analysis/tdeboer/galaxy-data/database2/tmp
> 
> 
> I set my TMPDIR environment variable to something similar, but when I check 
> what my python script is using as its temp dir I get this:
> 
> 
> print "Temp dir: %s" % tempfile.gettempdir()
> Temp dir: /tmp/3642962.1.all.q
> It seems that the SGE engine overrides the settings in GALAXY, no?
> So where do I set the tmp directory to be something different then /tmp?

Hi Thon,

Galaxy can't override SGE's setting of TMPDIR, it would have to happen 
somewhere in the execution of the job on the node.  You may be able to do this 
in the Galaxy user's .bash_profile, by modifying ~/.sge_request, or by setting 
up enviornment_setup_file in universe_wsgi.ini.

--nate

> 
> Thanks
> 
> Thon
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