-------- Original Message --------
Subject: Re: how to add settings of TMPDIR=/scratch for sge/drmaa in universe_wsgi.ini
Date:   Tue, 13 Aug 2013 23:21:16 -0700
From:   tin h <tin6...@gmail.com>
To:     Jennifer Jackson <j...@bx.psu.edu>
CC:     Galaxy Dev <galaxy-...@bx.psu.edu>




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 <http://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 <http://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 <http://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>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> <plugin id="sge" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
    </plugins>
    <destinations default="sge_default">
        <destination id="sge_default" runner="drmaa">
<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




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On 8/13/13 7:28 PM, Jennifer Jackson wrote:
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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