Thank you Jennifer.

I am not sure if my previous email got gabled up...

Just to be sure, I specified the following in universe_wsgi.ini

default_cluster_job_runner = drmaa://-q default.q -V -v TMPDIR=/scratch/

when i start galaxy, looking at the console log, this is what I see:

galaxy.jobs DEBUG 2013-08-14 14:08:14,885 Loaded job runner 'galaxy.jobs.runners.drmaa:DRMAAJobRunner' as 'drmaa'

galaxy.jobs.runners.drmaa DEBUG 2013-08-14 14:08:14,885 Converted URL 'drmaa://-q default.q -V -v TMPDIR=/scratch/' to destination runner=drmaa, params={'nativeSpecification': '-q default.q -V -v TMPDIR='}

galaxy.jobs DEBUG 2013-08-14 14:08:14,885 Legacy destination with id 'drmaa://-q default.q -V -v TMPDIR=/scratch/', url 'drmaa://-q default.q -V -v TMPDIR=/scratch/' converted, got params:

galaxy.jobs DEBUG 2013-08-14 14:08:14,885 nativeSpecification: -q default.q -V -v TMPDIR=

The parser has stopped at the / before scratch and ignored the rest :(

I did refer to http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster and tried to define job_conf.xml as

<?xml version="1.0"?>

<job_conf>

</plugins>

<param id="nativeSpecification">-q default.q -V -v TMPDIR=/scratch</param>

</destination>

</destinations>

</job_conf>

But then galaxy won't start, giving me the error of:

Traceback (most recent call last):

File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 37, in app_factory

app = UniverseApplication( global_conf = global_conf, **kwargs )

File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/app.py", line 95, in __init__

self.job_config = jobs.JobConfiguration(self)

File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 107, in __init__

self.__parse_job_conf_xml(tree)

File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 157, in __parse_job_conf_xml

self.default_handler_id = self.__get_default(handlers, self.handlers.keys())

File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 286, in __get_default

rval = parent.get('default')

AttributeError: 'NoneType' object has no attribute 'get'

I am not sure what the "default" refers to, doesn't seems to be the destinations default specified as I tried changing that name but the error message remains the same.

Any help so that I can pass TMPDIR=/scratch into SGE qsub would be greatly appreciated.

-Tin

I am riding to fundraise for the Cystic Fibrosis Foundation. Please consider a tax deductible donation at http://www.cff.org/LWC/dsp_DonationPage.cfm?idEvent=23815&idUser=615989

   ~~~            __o            Engineering is the art of making compromises.
         ~~~         _ <_             Science is the reverse engineering of the compromises made by nature.
       ~~~          (_)/(_)            Medicine is the hacking of the scientific knowledge base. - A comp sci student :-)

On Tue, Aug 13, 2013 at 7:28 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:

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,Â

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:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
-- Jennifer Hillman-Jackson http://galaxyproject.org