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Distribution of custom walker

dklevebringdklevebring Member
edited October 2013 in Ask the GATK team

Hi,

I have developed a custom walker that I think could be useful to the community. Therefore, I'd like to distribute it.

I tried following the brief guide "Redistributing the GATK-Lite or distributing walkers", but the building fails:

/Users/dankle/Dropbox/IdeaProjects/gatk/build.xml:955: no resources specified

The command I run is ant clean && ant package -Dexecutable=MyWalker.jar, and the xml-file in packages is

<package name="MyWalker">
  <version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
  <executable name="MyWalker">
    <main-class name="org.broadinstitute.sting.gatk.walkers.dk.MyWalker" />
    <resource-bundle file="StingText.properties" />
    <modules>
      <module file="GATKEngine.xml"/>
    </modules>
  </executable>
  <release>
    <executable directory="/humgen/gsa-hpprojects/GATK/bin" symlink="current" />
    <archive directory="/humgen/gsa-hpprojects/GATK/bin" symlink="GenomeAnalysisTK-latest.tar.bz2" />
  </release>
</package>

What am I doing wrong?

Daniel

Best Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    Hi Daniel,

    Cool, what does your walker do?

    Our developer docs are a little out of date so this might just be a case on incorrect instruction. I'll check with our software engineer in charge of builds, stay tuned.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer

    Hi Daniel,

    Cool, what does your walker do?

    Our developer docs are a little out of date so this might just be a case on incorrect instruction. I'll check with our software engineer in charge of builds, stay tuned.

  • Hey, that worked great. Thanks!

    @Geraldine_VdAuwera My walker is a dead-simple one that quantitates the telomeric content in one or more BAM files, on a per-sample basis. Something that can be very useful for whole-genome cancer samples.

    @droazen Related to distribution, I'd like to release the source code as well. The way I see it, I have two options.

    1) Something similar to how mutect is released, requiring a separate download of GATK for a user to compile.
    2) A "complete" gatk (public, not gatk-protected) release, which includes my walker among the other ones.

    The docs are a little ambious on which is preferred. I've not been able to set up IntelliJ properly to write walkers in a separate folder and them build them. However, adding a new walker and recompiling GenomeAnalysisTK with my walker being a part of it works great and is how I add my custom walkers now. Which is preferred?

    Or would you be interested in incorporating it in GATK?

    cheers
    Daniel

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Daniel,

    I'll discuss this with the team, but since we don't have the expertise to maintain your walker ourselves, it is unlikely that we will incorporate your walker into the "official" GATK; even though we think it's great that you wrote a walker for GATK (we really do!) -- this is a practical concern re: long-term maintenance of the code.

    So you can decide which option you prefer; bundling your walker into a fork of the core GATK (the "public"-only repo) and distributing that as a single jar, or following the MuTect model (which makes for a smaller download but does tend to confuse newbie users). We don't really have a preference, officially, that I'm aware of; personally I expect that the bundled version is easier for you to distribute and for users to use.

    In any case, we'd be happy to support your efforts to share your tools with the community; if you're interested we could host some documentation in the "Third-Party Tools" section of our website. And if you see a need for it, we could open a small forum section for you to field questions and feedback, if you don't have any other plans for a support platform (believe me, you don't want to do support over email).

  • Thanks, that sounds great. I'll work with the code a little while longer and run some more tests before releasing. I'll get back to you soon.

    Daniel

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Sure, take your time. When you are ready to release, if you are interested in having a small doc page/forum section for your tool, just let me know the name of your package and a brief description.

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