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Would it be possible for PbsEngine jobRunner not to set a default queue?

CarlosBorrotoCarlosBorroto Member Posts: 46
edited March 2014 in Ask the GATK team


I'm trying to use Queue with Torque through the PbsEngine jobRunner. The institutional cluster I'm trying to use doesn't allow users to select a queue. You are supposed to request the proper resources and a job routing algorithm selects the right queue for you.

I was able to confirm that doing this change allows me to use Queue in this kind of enviroment.

In "gatk-protected / public / queue-framework / src / main / scala / org / broadinstitute / sting / queue / engine / pbsengine / PbsEngineJobRunner.scala":


    // If the job queue is set specify the job queue
    if (function.jobQueue != null)
      nativeSpec += " -q " + function.jobQueue
      nativeSpec += " -q normal "


    // If the job queue is set specify the job queue
    if (function.jobQueue != null)
      nativeSpec += " -q " + function.jobQueue


PS: Do the GATK team accepts pull requests? If so, I could submit a pull request with this change.


Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,421 admin

    Sure, we accept pull requests. But I think this might need better handling for the case where you don't specify a queue but still need one to be set by default (?). Maybe it would be better to do this with a flag that deactivates setting the queue? I don't know if this makes sense and will defer to the usual experts of course :)

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,421 admin

    Hah, that is really helpful, thanks Phil. Yep, I was also reacting with the initial "undefined is bad" feeling, but if you tell me that's it's actually not (or not worse than an arbitrary and non-universal default) then I am quite happy with Carlos' solution.

    Carlos, feel free to make your pull-request to the public github repo and I'll make sure it gets processed. Please include the URL to this discussion in the description to fend off "undefined is bad" objections.

    Geraldine Van der Auwera, PhD

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