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95 lines
2.5 KiB
Nix
95 lines
2.5 KiB
Nix
{
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lib,
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stdenv,
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fetchFromGitHub,
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safestringlib,
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zlib,
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}:
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stdenv.mkDerivation (finalAttrs: {
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pname = "bwa-mem2";
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version = "unstable-2023-03-18";
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src = fetchFromGitHub {
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owner = "bwa-mem2";
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repo = "bwa-mem2";
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rev = "cf4306a47dac35e7e79a9e75398a35f33900cfd0";
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hash = "sha256-hY8nLRFWt0GAElhDIcYdUX6cJrzOE3NlYRQr0tC3on4=";
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};
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buildInputs = [ zlib ];
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buildFlags = [
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(
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if stdenv.hostPlatform.sse4_2Support then
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"arch=sse42"
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else if stdenv.hostPlatform.avxSupport then
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"arch=avx"
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else if stdenv.hostPlatform.avx2Support then
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"arch=avx2"
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else if stdenv.hostPlatform.avx512Support then
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"arch=avx512"
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else
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"arch=sse41"
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)
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];
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patches = [
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./no-submodule.patch
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];
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# Also, patch the tests
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postPatch =
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# Force path to static link, otherwise, it fails at runtime to
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# find the shared library
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''
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substituteInPlace Makefile \
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--replace-fail "-Iext/safestringlib/include" "-I${safestringlib}/include" \
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--replace-fail "-Lext/safestringlib" "-L${safestringlib}/lib"
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''
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# Make test compile by changing the compiler and path to library
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# Remove xeonbsw test that fails to compile due to missing _rdsc
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# also, not portable
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+ ''
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substituteInPlace test/Makefile \
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--replace-fail "icpc" "g++" \
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--replace-fail "../ext/safestringlib/libsafestring.a" \
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"${safestringlib}/lib/libsafestring.a" \
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--replace-fail \
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"fmi_test smem2_test bwt_seed_strategy_test sa2ref_test xeonbsw" \
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"fmi_test smem2_test bwt_seed_strategy_test sa2ref_test"
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'';
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env.NIX_CFLAGS_COMPILE = toString (
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lib.optionals stdenv.hostPlatform.isDarwin [
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"-Wno-error=register"
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"-Wno-error=implicit-function-declaration"
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]
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);
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nativeBuildInputs = [
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safestringlib
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];
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enableParallelBuilding = true;
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installPhase = ''
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runHook preInstall
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mkdir -p $out/bin
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cp bwa-mem2* $out/bin/
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runHook postInstall
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'';
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meta = with lib; {
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description = "Next version of the bwa-mem algorithm in bwa, a software package for mapping low-divergent sequences against a large reference genome";
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mainProgram = "bwa-mem2";
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license = licenses.mit;
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homepage = "https://github.com/bwa-mem2/bwa-mem2/";
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changelog = "https://github.com/bwa-mem2/bwa-mem2/blob/${finalAttrs.src.rev}/NEWS.md";
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platforms = platforms.x86_64;
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maintainers = with maintainers; [ apraga ];
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};
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})
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