On Wed, Jul 27, 2011 at 9:06 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
On Tue, Jul 26, 2011 at 8:16 PM, Luobin Yang yangluob@isu.edu wrote:
I benchmarked MrBayes 3.1.2 program on my cluster for two cases:
- use local /tmp for temporary files
- 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