pybedtools: Initial packaging

pkgs/pybedtools.nix

@@ -0,0 +1,32 @@
+{ lib, fetchFromGitHub, buildPythonPackage
+, 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
+  '';
+
+  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;
+  };
+}

pkgs/python-packages.nix

@@ -1,4 +1,6 @@
 pkgs: self: super: with self; {
 
   openslide = callPackage ./openslide/python.nix { openslide = pkgs.openslide; };
+
+  pybedtools = callPackage ./pybedtools.nix { };
 }