{ lib, fetchFromGitHub, buildPythonPackage, isPy3k
, cython, bedtools
, zlib, six, pysam, pytest, psutil, pyaml }:

buildPythonPackage rec {
  version = "0.8.0";
  name = "pybedtools-${version}";

  src = fetchFromGitHub {
    owner = "daler";
    repo = "pybedtools";
    rev = "v${version}";
    sha256 = "10c7rj07jz8v7r5yxfpwdx7dqfnrcncp16ry1y2cfk68awdnk122";
  };

  buildInputs = [ cython zlib ];
  propagatedBuildInputs = [ six pysam ];
  checkInputs = [ pytest psutil pyaml ];

  postPatch = ''
    sed -i -e '$ahelpers.set_bedtools_path('\'''${bedtools}/bin'\''')' pybedtools/__init__.py
  '';
  preBuild = ''
    python setup.py cythonize
  '';

  # TypeError: don't know how to make test from: <Logger pybedtools.logger (INFO)>
  doCheck = !isPy3k;

  meta = with lib; {
    homepage = "http://daler.github.io/pybedtools";
    description = "pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.";
    license = licenses.lgpl2Plus;
  };
}