63 lines
1.6 KiB
Nix
63 lines
1.6 KiB
Nix
{lib, stdenv, fetchFromGitHub, fetchpatch, cmake, boost, zlib, python2}:
|
|
|
|
stdenv.mkDerivation rec {
|
|
pname = "strelka";
|
|
version = "2.9.10";
|
|
|
|
src = fetchFromGitHub {
|
|
owner = "Illumina";
|
|
repo = "strelka";
|
|
rev = "v${version}";
|
|
sha256 = "1nykbmim1124xh22nrhrsn8xgjb3s2y7akrdapn9sl1gdych4ppf";
|
|
};
|
|
|
|
patches = [
|
|
# Pull pending fix for gcc-12:
|
|
# https://github.com/Illumina/strelka/pull/204
|
|
(fetchpatch {
|
|
name = "limits.patch";
|
|
url = "https://github.com/Illumina/strelka/commit/98272cd345c6e4c672e6a5b7721204fcac0502d6.patch";
|
|
hash = "sha256-psBiuN32nvwZ+QX51JQjIdRhEE3k7PfwbkD10ckqvZk=";
|
|
})
|
|
];
|
|
|
|
postPatch = ''
|
|
substituteInPlace src/cmake/boost.cmake \
|
|
--replace "1.58.0" "${boost.version}" \
|
|
--replace "Boost_USE_STATIC_LIBS ON" "Boost_USE_STATIC_LIBS OFF"
|
|
'';
|
|
|
|
nativeBuildInputs = [ cmake ];
|
|
buildInputs = [ boost zlib python2 ];
|
|
|
|
cmakeFlags = [
|
|
"-DCMAKE_CXX_STANDARD=14"
|
|
];
|
|
|
|
env.NIX_CFLAGS_COMPILE = toString [
|
|
"-Wno-error=maybe-uninitialized"
|
|
"-Wno-error=pessimizing-move"
|
|
];
|
|
|
|
preConfigure = ''
|
|
sed -i 's|/usr/bin/env python|${python2}/bin/python|' src/python/lib/makeRunScript.py
|
|
patchShebangs .
|
|
'';
|
|
|
|
postFixup = ''
|
|
pushd $out/lib/python/pyflow
|
|
sed -i 's|/bin/bash|${stdenv.shell}|' pyflowTaskWrapper.py
|
|
rm pyflowTaskWrapper.pyc
|
|
echo "import pyflowTaskWrapper" | python2
|
|
popd
|
|
'';
|
|
|
|
meta = with lib; {
|
|
description = "Germline and small variant caller";
|
|
license = licenses.gpl3;
|
|
homepage = "https://github.com/Illumina/strelka";
|
|
maintainers = with maintainers; [ jbedo ];
|
|
platforms = platforms.linux;
|
|
};
|
|
|
|
}
|