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truvari: init at 1.3.2 #70877

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merged 8 commits into from Oct 24, 2019
Merged

truvari: init at 1.3.2 #70877

merged 8 commits into from Oct 24, 2019

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scalavision
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Motivation for this change
Things done
  • [ x] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
  • Built on platform(s)
    • [x ] NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nix-review --run "nix-review wip"
  • [ x] Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • [ x] Ensured that relevant documentation is up to date
  • [ x] Fits CONTRIBUTING.md.
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The pyvcf license doesn't exclusively say MIT, but the text is identical as far as I can see.

I've created a specific version of the progressbar, don't know if any of the existing ones could be upgraded.

I upgraded the pysam library version to 0.15.3 to avoid creating a specific version for truvari. The differences of the versions seems to not have any compatibility issues.

Truvari is a much used tools for benchmarking within bioinformatics.

@ofborg ofborg bot requested a review from ashgillman October 9, 2019 19:20
@ashgillman
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ashgillman commented Oct 9, 2019 •
edited

You've used an older version of progressbar2 (note that progressbar and progressbar2 are separate projects, despite the latter being at major release 3.x 🙄 ). Can you try with the existing progressbar2 3.4.2?

@scalavision
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@ashgillman , thanks a lot for your help, finally I have been able to test this again locally, and now it works, also with this version of progressbar. Do you have any idea why the metaCheck is failing? I also get this failure in my other PR:

#70871

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veprbl commented Oct 10, 2019

Eval should be fixed by c0d5833
@GrahamcOfBorg eval

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Looks good to me :)

veprbl
veprbl reviewed Oct 11, 2019
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Not used

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scalavision commented Oct 11, 2019 •
edited

It was not possible to track what version of pyvcf on pypi matched the github repo, because there where no releases after 0.6.0. I've checked out from the last commit. From what I could see, the last changes are only test enhancements and bug fixes. I've tested truvari locally and it works.

Thanks a lot for helping out! I have learned a lot from this :-)

edit: I also added Spiral Genetics (the maker of the tool) to the long description in meta.

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FRidh commented Oct 24, 2019

@GrahamcOfBorg build truvari

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veprbl commented Oct 24, 2019

@GrahamcOfBorg build truvari

@veprbl veprbl merged commit 535a700 into NixOS:master Oct 24, 2019
jonringer pushed a commit that referenced this pull request Oct 25, 2019
@scalavision @jonringer
truvari: init at 1.3.2 (#70877)
455a266 
pythonPackages.pyvcf: init at 0.6.8
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@veprbl veprbl veprbl approved these changes

@ashgillman ashgillman ashgillman approved these changes

@FRidh FRidh Awaiting requested review from FRidh

@jonringer jonringer Awaiting requested review from jonringer

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