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

   1 {
   2   lib,
   3   fetchFromGitHub,
   4   rPackages,
   5   buildPythonPackage,
   6   biopython,
   7   numpy,
   8   scipy,
   9   scikit-learn,
  10   pandas,
  11   matplotlib,
  12   reportlab,
  13   pysam,
  14   future,
  15   pillow,
  16   pomegranate,
  17   pyfaidx,
  18   python,
  19   pythonOlder,
  20   R,
  21 }:
  22
  23 buildPythonPackage rec {
  24   pname = "cnvkit";
  25   version = "0.9.11";
  26   format = "setuptools";
  27
  28   disabled = pythonOlder "3.7";
  29
  30   src = fetchFromGitHub {
  31     owner = "etal";
  32     repo = "cnvkit";
  33     rev = "refs/tags/v${version}";
  34     hash = "sha256-tlR1LsR+M1nkzk3CgrkkNcSGP3juv25GXddWDDWJ5ao=";
  35   };
  36
  37   postPatch = ''
  38     # see https://github.com/etal/cnvkit/issues/589
  39     substituteInPlace setup.py \
  40       --replace 'joblib < 1.0' 'joblib'
  41     # see https://github.com/etal/cnvkit/issues/680
  42     substituteInPlace test/test_io.py \
  43       --replace 'test_read_vcf' 'dont_test_read_vcf'
  44   '';
  45
  46   propagatedBuildInputs = [
  47     biopython
  48     numpy
  49     scipy
  50     scikit-learn
  51     pandas
  52     matplotlib
  53     reportlab
  54     pyfaidx
  55     pysam
  56     future
  57     pillow
  58     pomegranate
  59     rPackages.DNAcopy
  60   ];
  61
  62   nativeCheckInputs = [ R ];
  63
  64   checkPhase = ''
  65     pushd test/
  66     ${python.interpreter} test_io.py
  67     ${python.interpreter} test_genome.py
  68     ${python.interpreter} test_cnvlib.py
  69     ${python.interpreter} test_commands.py
  70     ${python.interpreter} test_r.py
  71     popd # test/
  72   '';
  73
  74   pythonImportsCheck = [ "cnvlib" ];
  75
  76   meta = with lib; {
  77     homepage = "https://cnvkit.readthedocs.io";
  78     description = "Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data";
  79     changelog = "https://github.com/etal/cnvkit/releases/tag/v${version}";
  80     license = licenses.asl20;
  81     maintainers = [ maintainers.jbedo ];
  82   };
  83 }