fixes related to GATK bump to 3.8 #867
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| @@ -87,7 +87,7 @@ env_vars: | |||
| # The directory path to the location of the GATK jar file. | |||
| # It must be explicitly given since GATK has to be licensed and downloaded | |||
| # manually out of band. | |||
| GATK_PATH: "/humgen/gsa-hpprojects/GATK/bin/GenomeAnalysisTK-3.6-0-g89b7209" | |||
| GATK_PATH: "/idi/sabeti-scratch/shared-resources/software/gatk/GenomeAnalysisTK-3.8-0-ge9d806836" | |||
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Somewhat annoying there isn't an extracted directory for v3.8 within /humgen/gsa-hpprojects/GATK/bin. Should we ping someone upstairs?
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Another path to change is here:
https://github.com/broadinstitute/viral-ngs/blob/master/easy-deploy-script/easy-deploy-viral-ngs.sh#L282
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Thanks for catching these! |
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@tomkinsc I wonder why the standard travis-ci testing didn't catch these? |
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The easy-deploy script is no longer tested; I think it was taking too long. Otherwise, we set the |
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But the call to unified genotyper... that should've failed. Oh no, I know why... @tomkinsc when you updated GATK versions, did you also update the encrypted Travis tarball? Or is Travis still testing 3.6? |
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Actually instead of pulling the GATK jar from an encrypted Travis secret, I wonder if we can just pull it now from the no-longer-auth-protected GATK public URL... at least for Travis... |
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Shoot, I haven't updated it yet. |
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Yeah so... since the GATK team no longer protects their 3.x download URLs (and in fact, it looks like the gatk-protected github repo is now public?), we could replace this section of our install script with just |
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@tomkinsc Is https://github.com/broadinstitute/viral-ngs-deploy now obsolete? |
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Yeah we don't use that repo anymore... not since last fall. |
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@notestaff: Could you incorporate the Travis GATK |
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So actually... it looks like our travis setup no longer does anything with novoalign (we just test on the free/public version) so if we can get rid of the encrypted secret (like make the changes I suggested above and then also delete the three instances of BUNDLE_SECRET from .travis.yml) then people can actually run our python test suites on forks of our repo. Which would be nice. |
developer docs on upgrading GATK.
Removed GATK command-line args deprecated since 3.7 . Changed default path to GATK in pipes/config.yaml to point to a 3.8 version.