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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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