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How does the community manage custom walkers?

pdexheimerpdexheimer Member, Dev Posts: 543 ✭✭✭✭

I was wondering how other people package and manage any custom walkers they write? I wrote my first walker last week, and am now trying to figure out the best way to make it available to my team and keep it up to date with new versions of GATK. I do my development on a laptop and analysis on a cluster, so I have to sync the code somehow. I can think of two possibilities, it's unclear to me which is best:

Package a Monolithic jar

Pros: Makes distribution very easy, guarantees that there are never version compatibilities

Cons: Well, I haven't been able to do it yet. I can't quite figure out how to supply a package .xml file that will import my classes into GenomeAnalysisTK.jar (or Queue.jar, for that matter). Also, I think the version number will change when I customize it, and customers/collaborators may get confused about a non-standard version number (if they notice)

Create a "Custom Walker" jar

Pros: I know how to do it. It won't change the GATK version, so the log files won't look different

Cons: I'll have to remember to include my jar on the classpath (or set an environment variable, I suppose). It's possible to encounter version incompatibilities, for instance if I want to test 3.0 but use 2.8 for production

Now that I think it through, maybe the cons of the custom jar aren't as bad as I thought. Does anyone else have any experience with Custom Walker maintenance/deployment? How did you do it?


  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,993 admin

    Hi Phil,

    We have been porting GATK over to the Maven build system, which the softengs assure me will make this all much easier (starting in 3.0). We'll make sure to document the new build / distribution process. Eta next week.

    Geraldine Van der Auwera, PhD

  • pdexheimerpdexheimer Member, Dev Posts: 543 ✭✭✭✭

    You know, I've seen you mention that several times now, and I still spent several hours tracing and learning build.xml. Thanks, Geraldine - I'll table this for a day or so

    The larger question stands, though - does anyone feel like they're managing custom walkers well? What kind of problems/solutions have people encountered?

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