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Created 2014-03-21 22:43:33 | Updated 2014-03-21 22:44:48 | Tags: queue pbsengine
Comments (3)

Hi,

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":

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

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

Thanks, Carlos

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