Thanks Nate!

I did think that job_conf.xml would overwrite settings in
universe_wsgi.ini.  I rewrote it and see that the galaxy job gets to run on
the cluster.   However, the TMPDIR clause defined in nativeSpecification
didn't seems to be effective :(

the console output "log" does not show what the final nativeSpecification
was parsed as.  Given I didn't see any errors, I can assume that it was
taken as defined and it is SGE somehow not heeding the parameter?

Any other ideas of how I may fix this?  Or should I look at cluster
configuration to change it without relaying on galaxy?

relevant console output:

galaxy.jobs DEBUG 2013-08-16 02:50:51,622 Loading job configuration from
./job_conf.xml
galaxy.jobs DEBUG 2013-08-16 02:50:51,622 Read definition for handler 'main'
galaxy.jobs INFO 2013-08-16 02:50:51,623 Setting <handlers> default to
child with id 'main'
galaxy.jobs DEBUG 2013-08-16 02:50:51,623 <destinations> default set to
child with id or tag 'sge'
galaxy.jobs DEBUG 2013-08-16 02:50:51,623 Done loading job configuration
...
galaxy.jobs.manager DEBUG 2013-08-16 02:51:01,190 Starting job handler
galaxy.jobs.runners DEBUG 2013-08-16 02:51:01,192 Starting 4 LocalRunner
workers
galaxy.jobs DEBUG 2013-08-16 02:51:01,194 Loaded job runner
'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
galaxy.jobs.runners DEBUG 2013-08-16 02:51:01,242 Starting 4 DRMAARunner
workers
galaxy.jobs DEBUG 2013-08-16 02:51:01,243 Loaded job runner
'galaxy.jobs.runners.drmaa:DRMAAJobRunner' as 'drmaa'
galaxy.jobs.handler DEBUG 2013-08-16 02:51:01,243 Loaded job runners
plugins: drmaa:local
galaxy.jobs.handler INFO 2013-08-16 02:51:01,244 job handler stop queue
started
galaxy.jobs.handler INFO 2013-08-16 02:51:01,253 job handler queue started
...
galaxy.jobs DEBUG 2013-08-16 02:51:22,316 (218) Working directory for job
is: /usr/prog/galaxy/galaxy-dist/database/job_working_directory/000/218
galaxy.jobs.handler DEBUG 2013-08-16 02:51:22,320 (218) Dispatching to
drmaa runner
galaxy.jobs DEBUG 2013-08-16 02:51:22,399 (218) Persisting job destination
(destination id: sge)
galaxy.jobs.handler INFO 2013-08-16 02:51:22,415 (218) Job dispatched
galaxy.tools DEBUG 2013-08-16 02:51:22,648 Building dependency shell
command for dependency 'bwa'
galaxy.jobs.runners.drmaa DEBUG 2013-08-16 02:51:22,764 (218) submitting
file
/usr/prog/galaxy/galaxy-dist/database/job_working_directory/000/218/galaxy_218.sh
galaxy.jobs.runners.drmaa DEBUG 2013-08-16 02:51:22,765 (218) command is:
PACKAGE_BASE=/usr/prog/galaxy/tool_dependency/bwa/0.5.9/devteam/bwa_wrappers/150b3fe44caa;
export PACKAGE_BASE; .
/usr/prog/galaxy/tool_dependency/bwa/0.5.9/devteam/bwa_wrappers/150b3fe44caa/env.sh;
python /usr/prog/galaxy/shed_tools/
toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/150b3fe44caa/bwa_wrappers/bwa_wrapper.py
      --threads="4"         --fileSource="indexed"
--ref="/db/ngs-bioinfo/genomes/human/hg19/Homo_sapiens_assembly19.fasta"
      --do_not_build_index
 --input1="/usr/prog/galaxy/galaxy-dist/database/files/000/dataset_268.dat"

 --output="/usr/prog/galaxy/galaxy-dist/database/files/000/dataset_287.dat"
       --genAlignType="single"       --params="full"
--maxEditDist="0"         --fracMissingAligns="0.04"
--maxGapOpens="0"         --maxGapExtens="-1"
--disallowLongDel="16"         --disallowIndel="5"         --seed="-1"
    --maxEditDistSeed="2"         --mismatchPenalty="3"
--gapOpenPenalty="11"         --gapExtensPenalty="4"
--suboptAlign=""         --noIterSearch="false"         --outputTopN="3"
      --outputTopNDisc="10"         --maxInsertSize="500"
--maxOccurPairing="100000"        --suppressHeader="true"
galaxy.jobs.runners.drmaa INFO 2013-08-16 02:51:22,773 (218) queued as 37234
galaxy.jobs DEBUG 2013-08-16 02:51:22,805 (218) Persisting job destination
(destination id: sge)
galaxy.jobs.runners.drmaa DEBUG 2013-08-16 02:51:23,273 (218/37234) state
change: job is queued and active
galaxy.jobs.runners.drmaa DEBUG 2013-08-16 02:51:24,301 (218/37234) state
change: job is running




the updated job_conf.xml ::

<job_conf>
    <plugins>
        <plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
        <plugin id="drmaa" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
    </plugins>
    <handlers>
        <handler id="main"/>
    </handlers>
    <destinations default="sge">
        <destination id="sge" runner="drmaa">
                <!-- runner need to refer to a plugin id -->
                <param id="nativeSpecification">-q default.q -V -v
TMPDIR=/scratch</param>
        </destination>
        <destination id="local" runner="local"/>
    </destinations>
</job_conf>


Much thanks again,
-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 Thu, Aug 15, 2013 at 7:19 AM, Nate Coraor <n...@bx.psu.edu> wrote:

> 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 <j...@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 <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 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-...@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
> >>
> >>
> >> ___________________________________________________________
> >> Please keep all replies on the list by using "reply all"
> >> in your mail client.  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
> >
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  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/
>
>
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