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>
        <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 Tue, Aug 13, 2013 at 7:28 PM, Jennifer Jackson <j...@bx.psu.edu> 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,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
>
>
> ___________________________________________________________
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> --
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>
>
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