Hi Tin,

I am going to move this over to the galaxy-...@bx.psu.edu mailing list (good for local install questions) to give it better viability.


I am by no means the best person to help with this, so hopefully others will jump in, but just from looking at this I am wondering if you shouldn't be instead looking at the " job_conf.xml.sample_advanced" file. There is the default version as well, but it is probably not what you are looking for if you want to add custom logging scripts.

For universe_wsgi.ini, it seems like maybe the problem with the syntax is most likely the unknown "default_cluster_job_runner" variable and the double "=" in the line. Slashes should be fine unescaped here. But as I said, I think the other file is the place for the changes anyway, or maybe both, but using known variables and a single "=" per path.

But let's see what the developers think!

Jen
Galaxy team

On 8/12/13 3:49 PM, tin h wrote:

Hello galaxy gurus,Â

I am trying to configure a local galaxy server to submit to SGE using DRMAA, it works, but I would like to specify the equivalent of "-v TMPDIR=/scratch" for qsub.

I tried updating universe_wsgi.ini with something like:
 default_cluster_job_runner =  drmaa://-q default.q -V -v TMPDIR=/scratch/ but that doesn't work because "/" is a delimiter, and I have not been able to find way to escape it.  Is there any tricks for this?


Much thanks in advance for your help in this matter.
-Tin


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