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{
lib,
stdenv,
fetchFromGitHub,
simde,
zlib,
enableSse4_1 ? stdenv.hostPlatform.sse4_1Support,
enableAvx ? stdenv.hostPlatform.avxSupport,
enablePython ? false,
python3Packages,
runCommand,
abpoa,
}:
stdenv.mkDerivation (finalAttrs: {
pname = "${lib.optionalString enablePython "py"}abpoa";
version = "1.5.1";
src = fetchFromGitHub {
owner = "yangao07";
repo = "abPOA";
rev = "refs/tags/v${finalAttrs.version}";
hash = "sha256-nPMzkWkjUI+vZExNEvJa24KrR0pWGk89Mvp7TCyka/w=";
};
patches = [ ./simd-arch.patch ];
postPatch = ''
cp -r ${simde.src}/* include/simde
substituteInPlace Makefile \
--replace-fail "-march=native" ""
'';
nativeBuildInputs = lib.optionals enablePython (
with python3Packages;
[
cython
pypaBuildHook
pypaInstallHook
pythonImportsCheckHook
setuptools
]
);
buildFlags = lib.optionals stdenv.hostPlatform.isx86_64 [
(
if enableAvx then
"avx2=1"
else if enableSse4_1 then
"sse41=1"
else
"sse2=1"
)
];
env = lib.optionalAttrs enablePython (
if enableAvx then
{ "AVX2" = 1; }
else if enableSse4_1 then
{ "SSE41" = 1; }
else
{ "SSE2" = 1; }
);
buildInputs = [ zlib ];
installPhase = lib.optionalString (!enablePython) ''
runHook preInstall
install -Dm755 ./bin/abpoa -t $out/bin
runHook postInstall
'';
pythonImportsCheck = [ "pyabpoa" ];
doInstallCheck = enablePython;
installCheckPhase = ''
runHook preInstallCheck
python python/example.py
runHook postInstallCheck
'';
passthru.tests = {
simple = runCommand "${finalAttrs.pname}-test" { } ''
${lib.getExe abpoa} ${abpoa.src}/test_data/seq.fa > $out
'';
};
meta = with lib; {
description = "SIMD-based C library for fast partial order alignment using adaptive band";
homepage = "https://github.com/yangao07/abPOA";
changelog = "https://github.com/yangao07/abPOA/releases/tag/${finalAttrs.src.rev}";
license = licenses.mit;
maintainers = with maintainers; [ natsukium ];
mainProgram = "abpoa";
platforms = platforms.unix;
};
})
|
