96 lines
2.3 KiB
Nix
96 lines
2.3 KiB
Nix
|
{
|
||
|
|
lib,
|
||
|
|
config,
|
||
|
|
stdenv,
|
||
|
|
fetchFromGitHub,
|
||
|
|
cmake,
|
||
|
|
xxd,
|
||
|
|
perl,
|
||
|
|
installShellFiles,
|
||
|
|
enableAvx2 ? stdenv.hostPlatform.avx2Support,
|
||
|
|
enableSse4_1 ? stdenv.hostPlatform.sse4_1Support,
|
||
|
|
enableMpi ? false,
|
||
|
|
mpi,
|
||
|
|
cudaSupport ? config.cudaSupport,
|
||
|
|
cudaPackages,
|
||
|
|
llvmPackages,
|
||
|
|
zlib,
|
||
|
|
bzip2,
|
||
|
|
pkgsStatic,
|
||
|
|
runCommand,
|
||
|
|
}:
|
||
|
|
let
|
||
|
|
# require static library, libzstd.a
|
||
|
|
inherit (pkgsStatic) zstd;
|
||
|
|
in
|
||
|
|
|
||
|
|
stdenv.mkDerivation (finalAttrs: {
|
||
|
|
pname = "mmseqs2";
|
||
|
|
version = "18-8cc5c";
|
||
|
|
|
||
|
|
src = fetchFromGitHub {
|
||
|
|
owner = "soedinglab";
|
||
|
|
repo = "mmseqs2";
|
||
|
|
tag = finalAttrs.version;
|
||
|
|
hash = "sha256-xOdtAE6qpEOH13ubs7KEFAEwsYbB3a5t+QXTC+QxgLs=";
|
||
|
|
};
|
||
|
|
|
||
|
|
nativeBuildInputs = [
|
||
|
|
cmake
|
||
|
|
xxd
|
||
|
|
perl
|
||
|
|
installShellFiles
|
||
|
|
zstd
|
||
|
|
]
|
||
|
|
++ lib.optionals cudaSupport [
|
||
|
|
cudaPackages.cuda_nvcc
|
||
|
|
];
|
||
|
|
|
||
|
|
cmakeFlags = [
|
||
|
|
(lib.cmakeBool "HAVE_AVX2" enableAvx2)
|
||
|
|
(lib.cmakeBool "HAVE_SSE4_1" enableSse4_1)
|
||
|
|
(lib.cmakeBool "HAVE_MPI" enableMpi)
|
||
|
|
(lib.cmakeBool "USE_SYSTEM_ZSTD" true)
|
||
|
|
(lib.cmakeBool "HAVE_ARM8" stdenv.hostPlatform.isAarch64)
|
||
|
|
]
|
||
|
|
++ lib.optionals cudaSupport [
|
||
|
|
(lib.cmakeBool "ENABLE_CUDA" true)
|
||
|
|
(lib.cmakeFeature "CMAKE_CUDA_ARCHITECTURES" cudaPackages.flags.cmakeCudaArchitecturesString)
|
||
|
|
];
|
||
|
|
|
||
|
|
buildInputs =
|
||
|
|
lib.optionals stdenv.cc.isClang [
|
||
|
|
llvmPackages.openmp
|
||
|
|
zlib
|
||
|
|
bzip2
|
||
|
|
]
|
||
|
|
++ lib.optional enableMpi mpi
|
||
|
|
++ lib.optionals cudaSupport [
|
||
|
|
cudaPackages.cuda_cudart
|
||
|
|
cudaPackages.cuda_cccl
|
||
|
|
];
|
||
|
|
|
||
|
|
postInstall = ''
|
||
|
|
installShellCompletion --bash --cmd mmseqs $out/util/bash-completion.sh
|
||
|
|
rm -r $out/util/
|
||
|
|
'';
|
||
|
|
|
||
|
|
passthru.tests = {
|
||
|
|
example = runCommand "mmseqs2-test" { } ''
|
||
|
|
${lib.getExe finalAttrs.finalPackage} createdb ${finalAttrs.src}/examples/DB.fasta targetDB > $out
|
||
|
|
${lib.getExe finalAttrs.finalPackage} createindex targetDB tmp >> $out
|
||
|
|
${lib.getExe finalAttrs.finalPackage} easy-search ${finalAttrs.src}/examples/QUERY.fasta targetDB alnRes.m8 tmp >> $out
|
||
|
|
'';
|
||
|
|
};
|
||
|
|
|
||
|
|
meta = {
|
||
|
|
description = "Ultra fast and sensitive sequence search and clustering suite";
|
||
|
|
mainProgram = "mmseqs";
|
||
|
|
homepage = "https://mmseqs.com/";
|
||
|
|
changelog = "https://github.com/soedinglab/MMseqs2/releases/tag/${finalAttrs.version}";
|
||
|
|
license = lib.licenses.mit;
|
||
|
|
maintainers = with lib.maintainers; [ natsukium ];
|
||
|
|
platforms = lib.platforms.unix;
|
||
|
|
};
|
||
|
|
})
|