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?


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