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 else 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.