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Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

Obtaining the data used in automated tests in a more automated manner

bbimberbbimber HomePosts: 76

GATK has integration tests that depend on data, I presume all part of the GATK bundle. Is there anything in the build that downloads the expected data in a more automated manner than me manually downloading these to my computer? I assume something exists because you have automated testing, but I'm not seeing it. Thanks for any help.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAPosts: 11,743 admin
    Actually the test data is separate from the bundle, and where the test data lives is very different for GATK 3 vs GATK4. For 3 unfortunately we can't share it, it's on a private system. I know that sucks, we don't like it either. For 4 it's all public though I personally don't know how you access it. I would recommend asking in the github repo to get an answer directly from the devs who manage it.

    Geraldine Van der Auwera, PhD

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