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Running GATK from docker repository on Cancer Genomic Cloud (CGC)

Hello!

I'm having some problems running GATK on the Cancer Genomic Cloud (CGC) platform.
I've created my own tool using the following docker repository ''' broadinstitute/gatk:4.beta.5 '''
I'm using the following command line: ''' ./gatk-launch --javaOptions -d64 Mutect2 ''' etc. but the log file says ''' .2017-10-05T16:43:21.877696876Z sh: 1: ./gatk-launch: not found '''
I tried also using only ''' gatk-launch ''' with no results.
I thought there was an error in the repository path i wrote but it should be ok as, according to the log file, it seems it was opened correctly.

'''
2017-10-05 16:42:02: Download completed.
2017-10-05 16:42:02: Docker pull started. Image: broadinstitute/gatk:latest
2017-10-05 16:43:20: Docker pull completed.
2017-10-05 16:43:21: Starting docker container.
2017-10-05 16:43:21: Docker container started.
2017-10-05 16:43:21: Executing command: ./gatk-launch --javaOptions -d64 Mutect2 etc. etc. '''

thank you very much.

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator
    edited October 2017

    @Puputnik
    Hi,

    Can you clarify what you mean by "I tried also using only ''' gatk-launch ''' with no results." Did you try downloading the latest gatk4 from here and running Mutect2 on your own computer?

    Thanks,
    Sheila

    EDIT: If you did run Mutect2 on your own computer, can you post the error message/log output you get?

  • PuputnikPuputnik ItalyMember

    Hi Sheila,

    No, i didn't run Mutect2 on my computer, i meant i tried to use "gatk-launch" without "./"
    Anyway, i solved it, i was able to invoke it with "/*/gatk-launch"

    Thanks!

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