{ lib, fetchPypi, buildPythonApplication
, scipy, cytoolz, pysam
, pytest, pytestrunner }:

buildPythonApplication rec {
  version = "0.7.1";
  pname = "svtyper";

  src = fetchPypi {
    inherit pname version;
    sha256 = "1fryl5h947sf8rxj7pzrzjfy6is8xhq6yz25sd8hq88563mkianh";
  };

  postPatch = ''
    substituteInPlace setup.py \
      --replace o"pytest==4.6.4" "pytest"
  '';

  nativeBuildInputs = [ pytestrunner ];
  propagatedBuildInputs = [ scipy cytoolz pysam ];
  checkInputs = [ pytest ];

  # test infrastructure, but no tests in the package
  doCheck = false;

  meta = with lib; {
    homepage = https://github.com/hall-lab/svtyper;
    description = "Bayesian genotyper for structural variants.";
    license = licenses.mit;
  };
}