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.

Peter

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