depot/third_party/nixpkgs/pkgs/applications/science/biology/genmap/default.nix

{ lib
, stdenv
, fetchFromGitHub
, cmake
, gtest
, which
}:

stdenv.mkDerivation rec {
  pname = "genmap";
  version = "1.3.0";

  src = fetchFromGitHub {
    owner = "cpockrandt";
    repo = "genmap";
    rev = "genmap-v${version}";
    fetchSubmodules = true;
    hash = "sha256-7sIKBRMNzyCrZ/c2nXkknb6a5YsXe6DRE2IFhp6AviY=";
  };

  nativeBuildInputs = [ cmake ];

  doCheck = true;
  patches = [ ./gtest.patch ];
  nativeCheckInputs = [ gtest which ];
  preCheck = "make genmap_algo_test";

  # disable benchmarks
  preConfigure = ''
    echo > benchmarks/CMakeLists.txt
  '';

  meta = {
    description = "Ultra-fast computation of genome mappability";
    mainProgram = "genmap";
    license = lib.licenses.bsd3;
    homepage = "https://github.com/cpockrandt/genmap";
    maintainers = with lib.maintainers; [ jbedo ];
    platforms = lib.platforms.unix;
  };
}