Unverified Commit 57bd0c28 authored by Robert Scott's avatar Robert Scott Committed by GitHub
Browse files

Merge pull request #259413 from natsukium/truvari/update 

truvari: 4.0.0 -> 4.1.0; python311Packages.pywfa: init at 0.5.1
parents 45b469ec 96178c29

pkgs/applications/science/biology/truvari/default.nix

+9 −18
Original line number Diff line number Diff line 
{ lib

, fetchFromGitHub

, fetchpatch

, python3Packages

, runtimeShell

, bcftools
@@ -16,37 +15,28 @@ let 
  };

in python3Packages.buildPythonApplication rec {

  pname = "truvari";

  version = "4.0.0";

  version = "4.1.0";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "ACEnglish";

    repo = "truvari";

    rev = "v${version}";

    hash = "sha256-UJNMKEV5m2jFqnWvkVAtymkcE2TjPIXp7JqRZpMSqsE=";

    hash = "sha256-HFVAv1TTL/nMjr62tQKhMdwh25P/y4nBGzSbxoJxMmo=";

  };



  patches = [

    (fetchpatch {

      name = "fix-anno-trf-on-darwin.patch";

      url = "https://github.com/ACEnglish/truvari/commit/f9f36305e8eaa88f951562210e3672a4d4f71265.patch";

      hash = "sha256-7O9jTQDCC2b8hUBm0qJQCYMzTC9NFtn/E0dTHSfJALU=";

    })

    (fetchpatch {

      name = "fix-anno-grm-on-darwin.patch";

      url = "https://github.com/ACEnglish/truvari/commit/31416552008a506204ed4e2add55474f10392357.patch";

      hash = "sha256-42u0ewZU38GCoSfff+XQFv9hEFeO3WlJufTHcl6vkN4=";

    })

  ];



  postPatch = ''

    substituteInPlace setup.py \

      --replace "rich==" "rich>="

    substituteInPlace truvari/utils.py \

      --replace "/bin/bash" "${runtimeShell}"

    patchShebangs repo_utils/test_files

  '';



  nativeBuildInputs = [

    python3Packages.setuptools

  ];



  propagatedBuildInputs = with python3Packages; [

    pywfa

    rich

    edlib

    pysam
@@ -83,6 +73,7 @@ in python3Packages.buildPythonApplication rec { 
  meta = with lib; {

    description = "Structural variant comparison tool for VCFs";

    homepage = "https://github.com/ACEnglish/truvari";

    changelog = "https://github.com/ACEnglish/truvari/releases/tag/${src.rev}";

    license = licenses.mit;

    maintainers = with maintainers; [ natsukium scalavision ];

    longDescription = ''

pkgs/development/python-modules/pywfa/default.nix

0 → 100644
+53 −0
Original line number Diff line number Diff line 
{ lib

, buildPythonPackage

, fetchFromGitHub

, pythonOlder

, cython

, setuptools

, wheel

, pysam

, unittestCheckHook

}:



buildPythonPackage rec {

  pname = "pywfa";

  version = "0.5.1";

  pyproject = true;



  disabled = pythonOlder "3.7";



  src = fetchFromGitHub {

    owner = "kcleal";

    repo = "pywfa";

    rev = "refs/tags/v${version}";

    hash = "sha256-oeVXK9uyH4E98tApKrA7dXifQYb41KuDTAZ40XgAaF8=";

  };



  nativeBuildInputs = [

    cython

    setuptools

    wheel

  ];



  nativeCheckInputs = [

    pysam

    unittestCheckHook

  ];



  preCheck = ''

    cd pywfa/tests

  '';



  pythonImportsCheck = [

    "pywfa"

    "pywfa.align"

  ];



  meta = with lib; {

    description = "Python wrapper for wavefront alignment using WFA2-lib";

    homepage = "https://github.com/kcleal/pywfa";

    changelog = "https://github.com/kcleal/pywfa/releases/tag/${src.rev}";

    license = licenses.mit;

    maintainers = with maintainers; [ natsukium ];

  };

}

pkgs/top-level/python-packages.nix

+2 −0
Original line number Diff line number Diff line
@@ -11707,6 +11707,8 @@ self: super: with self; { 














  pywerview = callPackage ../development/python-modules/pywerview { };



























  pywfa = callPackage ../development/python-modules/pywfa { };



























  pywilight = callPackage ../development/python-modules/pywilight { };





























  pywinrm = callPackage ../development/python-modules/pywinrm { };