64 lines
2 KiB
Nix
64 lines
2 KiB
Nix
{ lib
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, stdenv
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, fetchFromGitHub
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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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fetchSubmodules = true;
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hash = "sha256-1AYSn7nBrDwbX7oSrdEoa1d3t6xzwKnA0S87Y/XeXJg=";
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};
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buildInputs = [ zlib ];
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# see https://github.com/bwa-mem2/bwa-mem2/issues/93
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postPatch = lib.optionalString stdenv.hostPlatform.isDarwin ''
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sed -i 's/memset_s/memset8_s/g' ext/safestringlib/include/safe_mem_lib.h
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sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset16_s.c
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sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset32_s.c
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sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset_s.c
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sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/wmemset_s.c
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'';
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buildFlags = [
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(if stdenv.hostPlatform.sse4_2Support then "arch=sse42"
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else if stdenv.hostPlatform.avxSupport then "arch=avx"
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else if stdenv.hostPlatform.avx2Support then "arch=avx2"
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else if stdenv.hostPlatform.avx512Support then "arch=avx512"
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else "arch=sse41")
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];
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env = lib.optionalAttrs stdenv.hostPlatform.isDarwin {
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NIX_CFLAGS_COMPILE = toString [
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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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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; [ alxsimon ];
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};
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})
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