Hi Tin, I am going to move this over to the galaxy-dev@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: Â default_cluster_job_runner = Â 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. Â Is there any tricks for this?
Much thanks in advance for your help in this matter. -Tin
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
-- Jennifer Hillman-Jackson http://galaxyproject.org