On Aug 14, 2013, at 9:46 PM, tin h wrote:

>
> Hello gurus,
>
>
> I made some slight progress...
>
> If I specify a handlers section into the job_conf.xml file with:
>     <handlers>
>         <handler id="main"/>
>     </handlers>
>
>
> Then galaxy would at least start.  However, it is not very functional, I can't upload files or run job, it says:
>
> An error occurred with this dataset:Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.
>
>
> My universe_wsgi.conf is fairly stock, the [server:main] section is certainly there.  The most relevant changes are:
>     start_job_runners = drmaa
>     default_cluster_job_runner =  drmaa://-q default.q -V -v TMPDIR=/scratch/
>
>
> If someone can point me to a job_conf.xml so that I can set the TMPDIR param correctly for qsub (sge), that would be greatly appreciated!
>
> Thanks
> -Tin

Hi Tin,

The start_job_runners and default_cluster_job_runner parameters are ignored once you switch to the new XML configuration.  The problem is most likely that the 'runner' attribute on your destination ("drmaa") does not match the 'id' attribute of the DRMAAJobRunner plugin ("sge"), so try changing one or the other so that they match.  More details regarding the error should be shown in the log.

--nate

>
>
>
>
> On Wed, Aug 14, 2013 at 8:04 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
> -------- 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
>
>
>
>
> --
>
> 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 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,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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>>
>> --
>> Jennifer Hillman-Jackson
>>
>> http://galaxyproject.org
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
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>
> --
> Jennifer Hillman-Jackson
>
> http://galaxyproject.org
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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>
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