SGE supports per-user defaults file called "~/.sge_request" , which can be used to set job's environment variables (and other qsub parameters). I think it was mentioned in the galaxy-dev list (I don't remember by whom). Example: ============ $ cat ~/.sge_request -v PERL5LIB=/data/hannon/gordon/perl_modules/lib64/perl5 -v DUMMY=HELLO ============ Will add two environment variables (PERL5LIB and DUMMY) to each qsub job. I guess this way you can also change the PATH. see "man sge_request" or "man ge_request" (in some places it is mentioned as "ge_request" instead of "sge_request"). "man qsub" tells which options take precedence ( command-line VS script VS user-sge_request VS gloval-sge_request ). Tested with SGE 6.1 and 6.2u3. -gordon Nate Coraor wrote, On 10/20/2009 11:51 AM:
Andreas Kuntzagk wrote:
It is set in ~/.bashrc, which is source by ~/.bash_profile. If I normally login to a cluster node via ssh it is set correctly. But if I qsub a job, it is not read. Except when I set the "-V" switch. So I either need to change gridengines behaviour or make galaxy use that switch.
Is there a easy way to config how to submit cluster jobs?
Andreas,
SGE must not be running the shell as a login or interactive shell, which PBS does. You may want to check the 'INVOCATION' section of the bash(1) man page to see how you can force this.
If you can't change how your shell is run by SGE, you could add what you need to the SGE job template in:
galaxy_dist/lib/galaxy/jobs/runners/sge.py
but this would be an ugly hack.
--nate _______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user