Peter Cock wrote:
> On Wed, Jul 27, 2011 at 9:06 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> > On Tue, Jul 26, 2011 at 8:16 PM, Luobin Yang <yangl...@isu.edu> wrote:
> >> I benchmarked MrBayes 3.1.2 program on my cluster for two cases:
> >> 1. use local /tmp for temporary files
> >> 2. use the network shared /home/galaxy/galaxy-dist/database/tmp
> >> MrBayes is about 10 times slower for case 2 than for case 1.  What I did 
> >> was
> >> to set the network shared folder as the default but in the MrBayes wrapper,
> >> I changed the environment variable TEMP to be a local folder.
> >> Luobin
> >
> > Does that mean Galaxy will configure the TEMP environment variable for
> > tools to point at the universe_wsgi.ini new_file_path setting? In your case,
> > /home/galaxy/galaxy-dist/database/tmp
> >
> > This is the kind of thing I think should be documented somewhere for
> > tool authors ...
> 
> ... and mentioned in the universe_wsgi.ini text for the new_file_path setting.
> 
> I've just seen Shantanu Pavgi's thread which also covers this issue, and
> the related TMP and TMPDIR environment variables set up or overridden
> by SGE. I think we agree that Galaxy needs some documentation and
> guidance in this area for tool authors.

Galaxy doesn't modify $TEMP, but in the past, setting $TEMP would cause
Galaxy to use that directory for all files created by Python's tempfile
module.  Since there was confusion over the difference between $TEMP
(which was documented as the way to control the creation of temp files)
and new_file_path, Galaxy was changed to put all temp files in the
location of new_file_path, ignoring $TEMP.

However, this only applies to the framework.  Tools run in a seperate
process and are not forced to use new_file_path.  If you want your tool
to use it, you could pass the value of new_file_path to your tool.

Otherwise, whatever rules are used by whatever you're using to create
temporary files will be what determines where temp files go; in Python,
it's this:

    http://docs.python.org/library/tempfile.html#tempfile.tempdir

Our cluster nodes have the majority of their local disk partitioned as
/space, so we set TEMP=/space in the environment used on the nodes.

--nate

> 
> Peter
> 
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