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Running GATK-Queue in SLURM

Hi,

I am trying to run GATK-QUEUE in SLURM environment. But I couldn't find any instruction that shows how to run it. How can I run it in SLURM environment?

Thanks,
Mucahid

Best Answer

Answers

  • mkutlumkutlu Member
    edited June 2013

    I figured out how to do it in SLURM environment. Maybe it helps others.

    1- slurm-drmaa should be downloaded.

    2- PATH should be set: export LD_LIBRARY_PATH= YOUR_SLURM_DRMAA_LIB_PATH:$LD_LIBRARY_PATH

    3- jobRunner parameter should be set to Drmaa. Walltime can/should be set to a value(not sure if it is mandatory).
    java -Djava.io.tmpdir=tmp -jar queue.jar -S example.scala -I INPUT -R REFERENCE_FILE -jobRunner Drmaa --job_walltime SOME_NUMERIC_VALUE -run

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Thanks for sharing your solution!

  • medhatmedhat PolandMember

    @mkutlu

    java -Djava.io.tmpdir=tmp -jar queue.jar -S example.scala -I INPUT -R REFERENCE_FILE -jobRunner Drmaa --job_walltime SOME_NUMERIC_VALUE -run

    what about number of cores, tasks and cpu shoukd it be stated in the command line or the shell script runed by sbatch?

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