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Merge pull request #248172 from alxsimon/bwa

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bwa-mem2: init at version 2.2.1
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OTABI Tomoya 2023-08-24 09:28:34 +09:00 committed by GitHub
parent dfe898c801 556dac0725
commit 21943b1829
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55
pkgs/applications/science/biology/bwa-mem2/default.nix Normal file
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@ -0,0 +1,55 @@
{ lib
, stdenv
, fetchFromGitHub
, zlib
}:
stdenv.mkDerivation (finalAttrs: {
pname = "bwa-mem2";
version = "unstable-2023-03-18";
src = fetchFromGitHub {
owner = "bwa-mem2";
repo = "bwa-mem2";
rev = "cf4306a47dac35e7e79a9e75398a35f33900cfd0";
fetchSubmodules = true;
hash = "sha256-1AYSn7nBrDwbX7oSrdEoa1d3t6xzwKnA0S87Y/XeXJg=";
};
buildInputs = [ zlib ];
# see https://github.com/bwa-mem2/bwa-mem2/issues/93
postPatch = lib.optionalString stdenv.isDarwin ''
sed -i 's/memset_s/memset8_s/g' ext/safestringlib/include/safe_mem_lib.h
sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset16_s.c
sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset32_s.c
sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset_s.c
sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/wmemset_s.c
'';
buildFlags = [
(if stdenv.hostPlatform.sse4_2Support then "arch=sse42"
else if stdenv.hostPlatform.avxSupport then "arch=avx"
else if stdenv.hostPlatform.avx2Support then "arch=avx2"
else if stdenv.hostPlatform.avx512Support then "arch=avx512"
else "arch=sse41")
];
enableParallelBuilding = true;
installPhase = ''
runHook preInstall
mkdir -p $out/bin
cp bwa-mem2* $out/bin/
runHook postInstall
'';
meta = with lib; {
description = "Next version of the bwa-mem algorithm in bwa, a software package for mapping low-divergent sequences against a large reference genome";
license = licenses.mit;
homepage = "https://github.com/bwa-mem2/bwa-mem2/";
changelog = "https://github.com/bwa-mem2/bwa-mem2/blob/${finalAttrs.src.rev}/NEWS.md";
platforms = platforms.x86_64;
maintainers = with maintainers; [ alxsimon ];
};
})

2
pkgs/top-level/all-packages.nix
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@ -39144,6 +39144,8 @@ with pkgs;
bwa = callPackage ../applications/science/biology/bwa { };
bwa-mem2 = callPackage ../applications/science/biology/bwa-mem2 { };
### SCIENCE/MACHINE LEARNING
nengo-gui = callPackage ../applications/science/machine-learning/nengo-gui { };