pkgs/by-name/fl/flye/package.nix

   1 {
   2   lib,
   3   fetchFromGitHub,
   4   fetchpatch,
   5   python3Packages,
   6   zlib,
   7   curl,
   8   libdeflate,
   9   bash,
  10   coreutils,
  11   addBinToPathHook,
  12 }:
  13
  14 python3Packages.buildPythonApplication rec {
  15   pname = "flye";
  16   version = "2.9.5";
  17   pyproject = true;
  18
  19   src = fetchFromGitHub {
  20     owner = "fenderglass";
  21     repo = "flye";
  22     tag = version;
  23     hash = "sha256-448PTdGueQVHFIDS5zMy+XKZCtEb0SqP8bspPLHMJn0=";
  24   };
  25
  26   patches = [
  27     (fetchpatch {
  28       # https://github.com/mikolmogorov/Flye/pull/691
  29       name = "aarch64-fix.patch";
  30       url = "https://github.com/mikolmogorov/Flye/commit/e4dcc3fdf0fa1430a974fcd7da31b03ea642df9b.patch";
  31       hash = "sha256-Ny2daPt8eYOKnwZ6bdBoCcFWhe9eiIHF4vJU/occwU0=";
  32     })
  33     (fetchpatch {
  34       # https://github.com/mikolmogorov/Flye/pull/711
  35       name = "remove-distutils.patch";
  36       url = "https://github.com/mikolmogorov/Flye/commit/fb34f1ccfdf569d186a4ce822ee18eced736636b.patch";
  37       hash = "sha256-52bnZ8XyP0HsY2OpNYMU3xJgotNVdQc/O2w3XIReUdQ=";
  38     })
  39   ];
  40
  41   postPatch = ''
  42     substituteInPlace flye/polishing/alignment.py \
  43       --replace-fail "/bin/bash" "${lib.getExe bash}"
  44   '';
  45
  46   build-system = [ python3Packages.setuptools ];
  47
  48   propagatedBuildInputs = [ coreutils ];
  49
  50   buildInputs = [
  51     zlib
  52     curl
  53     libdeflate
  54   ];
  55
  56   pythonImportsCheck = [ "flye" ];
  57
  58   nativeCheckInputs = [
  59     addBinToPathHook
  60     python3Packages.pytestCheckHook
  61   ];
  62
  63   meta = with lib; {
  64     description = "De novo assembler for single molecule sequencing reads using repeat graphs";
  65     homepage = "https://github.com/fenderglass/Flye";
  66     license = licenses.bsd3;
  67     mainProgram = "flye";
  68     maintainers = with maintainers; [ assistant ];
  69   };
  70 }