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