svtyper: Initial packaging

pkgs/all-packages.nix

@@ -56,6 +56,8 @@ self: super: pkgs: with pkgs; {
 
   samblaster = callPackage ./samblaster.nix { };
 
+  svtyper = pythonPackages.callPackage ./svtyper.nix { };
+
   idba = callPackage ./idba.nix { };
 
   nixStable = ( super.nixStable.override { confDir= "/nix/etc"; } ).overrideAttrs

pkgs/svtyper.nix

@@ -0,0 +1,31 @@
+{ 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;
+  };
+}