If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

MuTect Build Problem

kcibulkcibul Cambridge, MAMember, Broadie, Dev ✭✭✭
This discussion was created from comments split from: MuTect source now available in GitHub!.


  • andreandre Member

    Hi, I try to follow the build intructions in the MuTect github Readme. It seems to build fine but the packaging does not work (see log attached). When I do a "dist" instead of "package" ant runs through but the only classes related to MuTect in the jar seem to be the queue extensions. Strange.. I wonder if I am doing something wrong?

  • kcibulkcibul Cambridge, MAMember, Broadie, Dev ✭✭✭

    Hi -- I'm not sure what the trouble is that you're having. I just took the instructions from the GitHub Readme and ran them on a clean machine and everything was ok.

    I noticed in your build output it says:

     [echo] Include External?  : no

    Which means either you didn't run with the specified command (ant -Dexternal.dir=pwd/../mutect-src -Dexecutable=mutect package)
    or that the mutect-src isn't in the right place relative to the gatk dir. the external.dir above should point to the directory ABOVE the mutect directory. So if you run "ls -l pwd/../mutect-src" you will see:

    bm5fb-3a0:~/andre/gatk-protected [master*] $ ls -l pwd/../mutect-src
    total 0
    drwxr-xr-x 14 kcibul CHARLES\Domain Users 476 Oct 25 21:14 mutect

    Hope this helps

  • andreandre Member

    Thanks for the help. Actually it was an issue with the directory structure. So just for reference, the correct one ist:

    top_level /mutect-src /mutect /gatk-protected

    I probably got confused by the order in which the two repositories are cloned. Anyway, thanks again.

Sign In or Register to comment.