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:
http://lists.bx.psu.edu/
___
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:
http://lists.bx.psu.edu/
