pkgs/by-name/ma/manta/package.nix

   1 { lib, stdenv, fetchFromGitHub, cmake, zlib, python2 }:
   2
   3 stdenv.mkDerivation rec {
   4   pname = "manta";
   5   version = "1.6.0";
   6
   7   src = fetchFromGitHub {
   8     owner = "Illumina";
   9     repo = "manta";
  10     rev = "v${version}";
  11     sha256 = "1711xkcw8rpw9xv3bbm7v1aryjz4r341rkq5255192dg38sgq7w2";
  12   };
  13
  14   nativeBuildInputs = [ cmake ];
  15   buildInputs = [ zlib python2 ];
  16   postFixup = ''
  17     sed -i 's|/usr/bin/env python2|${python2.interpreter}|' $out/lib/python/makeRunScript.py
  18     sed -i 's|/usr/bin/env python|${python2.interpreter}|' $out/lib/python/pyflow/pyflow.py
  19     sed -i 's|/bin/bash|${stdenv.shell}|' $out/lib/python/pyflow/pyflowTaskWrapper.py
  20   '';
  21   doInstallCheck = true;
  22   installCheckPhase = ''
  23     rm $out/lib/python/**/*.pyc
  24     PYTHONPATH=$out/lib/python:$PYTHONPATH python -c 'import makeRunScript'
  25     PYTHONPATH=$out/lib/python/pyflow:$PYTHONPATH python -c 'import pyflowTaskWrapper; import pyflow'
  26   '';
  27
  28   env.NIX_CFLAGS_COMPILE = "-Wno-error=array-bounds";
  29
  30   meta = with lib; {
  31     description = "Structural variant caller";
  32     license = licenses.gpl3;
  33     homepage = "https://github.com/Illumina/manta";
  34     maintainers = with maintainers; [ jbedo ];
  35     platforms =  platforms.x86_64;
  36   };
  37 }