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truvari: 1.3.4 -> 2.0.2, add new dependencies & fix build #98283

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merged 5 commits into from Sep 23, 2020
Merged

truvari: 1.3.4 -> 2.0.2, add new dependencies & fix build #98283

merged 5 commits into from Sep 23, 2020

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risicle
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@risicle risicle commented Sep 19, 2020

Motivation for this change

Possibly ZHF: #97479

This is an alternative to #98250 where I simply minimally fixed the exitsing truvari. This bumps it to 2.0.2 and adds new python dependencies bwapy, pytabix and acebinf. Also needed to expose the compiled library in the bwa package.

Not sure which we want to use. Could do the minimal bump for 20.09 and keep this for master.

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
  • Built on platform(s)
    • 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 nixpkgs-review --run "nixpkgs-review wip"
  • 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)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.

@risicle risicle mentioned this pull request Sep 19, 2020
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10 tasks
@ofborg ofborg bot requested a review from luispedro September 19, 2020 17:23
@jonringer
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there seem to be some conflicts :(

@risicle
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risicle commented Sep 20, 2020

Yup, this is because #98250 was merged, which was my alternate take on this problem. That's good, because I can easily fix this one up, get it in master and then choose whether to port just the basic fix to 20.09 or bring the bump too.

jonringer
jonringer reviewed Sep 22, 2020
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pkgs/development/python-modules/pytabix/default.nix
Comment on lines +19 to +23
doCheck = !isPy3k;
preCheck = ''
substituteInPlace test/test.py \
--replace 'test_remote_file' 'dont_test_remote_file'
'';
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not sure why this is still being ran for python2:

https://github.com/NixOS/nixpkgs/pull/98283
1 package failed to build:
python27Packages.pytabix

10 packages built:
bwa python27Packages.acebinf python37Packages.acebinf python37Packages.bwapy python37Packages.pytabix python38Packages.acebinf python38Packages.bwapy python38Packages.pytabix tebreak truvari

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nevermind, i read that right

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That's .. strange. What was the failure? An earlier version of this PR didn't disable the tests on py27, but this version builds for me on macos 10.14 & linux under nixpkgs-review.

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I believe it was an encoding error:

....
but I can no longer reproduce it....

https://github.com/NixOS/nixpkgs/pull/98283
11 packages built:
bwa python27Packages.acebinf python27Packages.pytabix python37Packages.acebinf python37Packages.bwapy python37Packages.pytabix python38Packages.acebinf python38Packages.bwapy python38Packages.pytabix tebreak truvari

jonringer
jonringer approved these changes Sep 23, 2020
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diff LGTM

https://github.com/NixOS/nixpkgs/pull/98283
11 packages built:
bwa python27Packages.acebinf python27Packages.pytabix python37Packages.acebinf python37Packages.bwapy python37Packages.pytabix python38Packages.acebinf python38Packages.bwapy python38Packages.pytabix tebreak truvari

pkgs/applications/science/biology/bwa/default.nix
Comment on lines +19 to +22
install -vD -t $out/include bntseq.h
install -vD -t $out/include bwa.h
install -vD -t $out/include bwamem.h
install -vD -t $out/include bwt.h
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I don't feel strongly though

Suggested change
install -vD -t $out/include bntseq.h
install -vD -t $out/include bwa.h
install -vD -t $out/include bwamem.h
install -vD -t $out/include bwt.h
install -vD -t $out/include bntseq.h bwa.h bwamem.h bwt.h

pkgs/development/python-modules/pytabix/default.nix
Comment on lines +19 to +23
doCheck = !isPy3k;
preCheck = ''
substituteInPlace test/test.py \
--replace 'test_remote_file' 'dont_test_remote_file'
'';
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I believe it was an encoding error:

....
but I can no longer reproduce it....

https://github.com/NixOS/nixpkgs/pull/98283
11 packages built:
bwa python27Packages.acebinf python27Packages.pytabix python37Packages.acebinf python37Packages.bwapy python37Packages.pytabix python38Packages.acebinf python38Packages.bwapy python38Packages.pytabix tebreak truvari

@jonringer jonringer merged commit c7fdc43 into NixOS:master Sep 23, 2020
@risicle risicle mentioned this pull request Sep 23, 2020
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@jonringer jonringer jonringer approved these changes

@FRidh FRidh Awaiting requested review from FRidh

@luispedro luispedro Awaiting requested review from luispedro

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