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571c71e6f7
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64 lines
1.6 KiB
Nix
64 lines
1.6 KiB
Nix
{lib, stdenv, fetchFromGitHub, fetchpatch, cmake, boost, zlib, python2}:
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stdenv.mkDerivation rec {
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pname = "strelka";
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version = "2.9.10";
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src = fetchFromGitHub {
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owner = "Illumina";
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repo = "strelka";
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rev = "v${version}";
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sha256 = "1nykbmim1124xh22nrhrsn8xgjb3s2y7akrdapn9sl1gdych4ppf";
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};
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patches = [
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# Pull pending fix for gcc-12:
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# https://github.com/Illumina/strelka/pull/204
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(fetchpatch {
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name = "limits.patch";
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url = "https://github.com/Illumina/strelka/commit/98272cd345c6e4c672e6a5b7721204fcac0502d6.patch";
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hash = "sha256-psBiuN32nvwZ+QX51JQjIdRhEE3k7PfwbkD10ckqvZk=";
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})
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];
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postPatch = ''
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substituteInPlace src/cmake/boost.cmake \
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--replace "1.58.0" "${boost.version}" \
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--replace "Boost_USE_STATIC_LIBS ON" "Boost_USE_STATIC_LIBS OFF"
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'';
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nativeBuildInputs = [ cmake ];
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buildInputs = [ boost zlib python2 ];
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cmakeFlags = [
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"-DCMAKE_CXX_STANDARD=14"
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];
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env.NIX_CFLAGS_COMPILE = toString [
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"-Wno-error=maybe-uninitialized"
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"-Wno-error=pessimizing-move"
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];
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preConfigure = ''
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sed -i 's|/usr/bin/env python|${python2}/bin/python|' src/python/lib/makeRunScript.py
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patchShebangs .
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'';
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postFixup = ''
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pushd $out/lib/python/pyflow
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sed -i 's|/bin/bash|${stdenv.shell}|' pyflowTaskWrapper.py
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rm pyflowTaskWrapper.pyc
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echo "import pyflowTaskWrapper" | python2
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popd
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'';
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meta = with lib; {
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description = "Germline and small variant caller";
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license = licenses.gpl3;
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homepage = "https://github.com/Illumina/strelka";
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maintainers = with maintainers; [ jbedo ];
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platforms = platforms.linux;
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};
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}
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