Commit dab389b7 authored by Gaetan Lepage's avatar Gaetan Lepage
Browse files

hap-py: cleanup, fix cmake 4 compatibility

parent 7e09866f

pkgs/by-name/ha/hap-py/package.nix

+27 −13
Original line number Diff line number Diff line
@@ -37,22 +37,26 @@ let 
    ];

  my-python = python3.withPackages my-python-packages;

in

stdenv.mkDerivation rec {

stdenv.mkDerivation (finalAttrs: {

  pname = "hap.py";

  version = "0.3.15";



  src = fetchFromGitHub {

    owner = "Illumina";

    repo = "hap.py";

    rev = "v${version}";

    tag = "v${finalAttrs.version}";

    hash = "sha256-K8XXhioMGMHw56MKvp0Eo8S6R36JczBzGRaBz035zRQ=";

  };

  # For illumina script

  BOOST_ROOT = "${boost.out}";

  ZLIBSTATIC = "${zlib.static}";

  # For cmake : boost lib and includedir are in different location

  BOOST_LIBRARYDIR = "${boost.out}/lib";

  BOOST_INCLUDEDIR = "${boost.dev}/include";



  # CMake 4 dropped support of versions lower than 3.5,

  # versions lower than 3.10 are deprecated.

  # https://github.com/NixOS/nixpkgs/issues/445447

  postPatch = ''

    substituteInPlace CMakeLists.txt \

      --replace-fail \

        "cmake_minimum_required (VERSION 2.8)" \

        "cmake_minimum_required (VERSION 3.10)"

  '';



  patches = [

    # Compatibility with nix for boost and library flags : zlib, bzip2, curl, crypto, lzma
@@ -76,17 +80,27 @@ stdenv.mkDerivation rec { 
    zlib

  ];



  env = {

    # For illumina script

    BOOST_ROOT = "${boost.out}";

    ZLIBSTATIC = "${zlib.static}";



    # For cmake : boost lib and includedir are in different location

    BOOST_LIBRARYDIR = "${boost.out}/lib";

    BOOST_INCLUDEDIR = "${boost.dev}/include";

  };



  postFixup = ''

    wrapProgram $out/bin/hap.py \

       --set PATH ${lib.makeBinPath runtime} \

       --add-flags "--engine-vcfeval-path=${rtg-tools}/bin/rtg"

       --add-flags "--engine-vcfeval-path=${lib.getExe rtg-tools}"

  '';



  meta = with lib; {

  meta = {

    description = "Compare genetics variants against a gold dataset";

    homepage = "https://github.com/Illumina/hap.py";

    license = licenses.bsd2;

    maintainers = with maintainers; [ apraga ];

    license = lib.licenses.bsd2;

    maintainers = with lib.maintainers; [ apraga ];

    mainProgram = "hap.py";

  };

}
 
})