blob: ad6c0d9e5a4cc730bdb30620e13dcad228e5f81c (
plain) (
blame)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
|
{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;
};
}
|
