pkgs/applications/science/biology/strelka/default.nix

   1 {lib, stdenv, fetchFromGitHub, fetchpatch, cmake, boost, zlib, python2}:
   2
   3 stdenv.mkDerivation rec {
   4   pname = "strelka";
   5   version = "2.9.10";
   6
   7   src = fetchFromGitHub {
   8     owner = "Illumina";
   9     repo = "strelka";
  10     rev = "v${version}";
  11     sha256 = "1nykbmim1124xh22nrhrsn8xgjb3s2y7akrdapn9sl1gdych4ppf";
  12   };
  13
  14   patches = [
  15     # Pull pending fix for gcc-12:
  16     #   https://github.com/Illumina/strelka/pull/204
  17     (fetchpatch {
  18       name = "limits.patch";
  19       url = "https://github.com/Illumina/strelka/commit/98272cd345c6e4c672e6a5b7721204fcac0502d6.patch";
  20       hash = "sha256-psBiuN32nvwZ+QX51JQjIdRhEE3k7PfwbkD10ckqvZk=";
  21     })
  22   ];
  23
  24   postPatch = ''
  25     substituteInPlace src/cmake/boost.cmake \
  26       --replace "1.58.0" "${boost.version}" \
  27       --replace "Boost_USE_STATIC_LIBS ON" "Boost_USE_STATIC_LIBS OFF"
  28   '';
  29
  30   nativeBuildInputs = [ cmake ];
  31   buildInputs = [ boost zlib python2 ];
  32
  33   cmakeFlags = [
  34     "-DCMAKE_CXX_STANDARD=14"
  35   ];
  36
  37   env.NIX_CFLAGS_COMPILE = toString [
  38     "-Wno-error=maybe-uninitialized"
  39     "-Wno-error=pessimizing-move"
  40   ];
  41
  42   preConfigure = ''
  43     sed -i 's|/usr/bin/env python|${python2}/bin/python|' src/python/lib/makeRunScript.py
  44     patchShebangs .
  45   '';
  46
  47   postFixup = ''
  48     pushd $out/lib/python/pyflow
  49     sed -i 's|/bin/bash|${stdenv.shell}|' pyflowTaskWrapper.py
  50     rm pyflowTaskWrapper.pyc
  51     echo "import pyflowTaskWrapper" | python2
  52     popd
  53   '';
  54
  55   meta = with lib; {
  56     description = "Germline and small variant caller";
  57     license = licenses.gpl3;
  58     homepage = "https://github.com/Illumina/strelka";
  59     maintainers = with maintainers; [ jbedo ];
  60     platforms = platforms.linux;
  61   };
  62
  63 }