-------- 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 <tin6150@gmail.com>
To:	Jennifer Jackson <jen@bx.psu.edu>
CC:	Galaxy Dev <galaxy-dev@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 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 8/13/13 7:28 PM, Jennifer Jackson 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, 

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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