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  • Galaxy & SGE

    Hi, all.

    We have constructed Galaxy with SGE.

    The problem is that we cannot specify execution queue in job_conf.xml.
    The job_conf.xml is as following, and please ignore numbers in top of lines.

    We set "cluster" the default destination in #11. and "nativeSpecification" in "cluster" '-q N.q'.

    In our SGE, the queue, 'N.q' has already created and we can submit a job into 'N.q' by qsub command.

    However, we start a job in our Galaxy, the job is submitted into the other queue.

    When we designate '-q L.q', in "nativeSpecification", the job is submitted into this queue.
    The queue L.q is another queue in our SGE, and it had been already created.

    We would like to submit a job into the queue N.q.

    Can we ask some advice?

    ----
    NAMIKI Nobukazu

    Code:
      1 <plugins>
      2   <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="8"/>
      3   <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
      4     <!-- Override the $DRMAA_LIBRARY_PATH environment variable -->
      5     <param id="drmaa_library_path">/xxxxx/libdrmaa.so.1.0</param>
      6   </plugin>
      7 </plugins>
      8 <handlers>
      9   <handler id="main"/>
     10 </handlers>
     11 <destinations default="cluster">
     12    <destination id="local" runner="local"/>
     13    <destination id="cluster" runner="drmaa">
     14       <param id="nativeSpecification">-q N.q</param>
     15     </destination>
     16     <destination id="Large" runner="drmaa">
     17       <param id="nativeSpecification">-q gL.q -pe smp 4</param>
     18     </destination>

  • #2
    Namiki,

    I "borrowed" this from a friend who has Galaxy submitting properly to his cluster...not sure if it will be of any help or not...

    <?xml version="1.0"?>
    <job_conf>
    <plugins>
    <plugin id="hpccqueue" type="runner" load="galaxy.jobs.runners.drmaaRMAAJobRunner"/>
    </plugins>
    <handlers>
    <handler id="main"/>
    </handlers>
    <destinations>
    <destination id="hpcc_default" runner="hpccqueue">
    <param id="nativeSpecification">-l walltime=3:59:00</param>
    </destination>
    </destinations>
    </job_conf>

    Comment


    • #3
      Sorry, smiley face was supposed to be a colon ":"

      Forum changed it to an emoticon...

      Comment


      • #4
        Originally posted by jpummil View Post
        Sorry, smiley face was supposed to be a colon ":"

        Forum changed it to an emoticon...
        Choose "Edit" --> "Go Advanced" and then you can either manually add [CODE] actual code goes here [/ CODE] (remove the space between / and CODE) tags around the code OR high-light the code and then click on the "#" icon in the menu bar to add the CODE tags automatically.

        Comment

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