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Merge pull request #191023 from cesarpomar/master
veryfasttree 4.0.4 (new formula)
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| class Veryfasttree < Formula | ||
| desc "Efficient phylogenetic tree inference for massive taxonomic datasets" | ||
| homepage "https://github.com/citiususc/veryfasttree" | ||
| url "https://github.com/citiususc/veryfasttree/archive/refs/tags/v4.0.4.tar.gz" | ||
| sha256 "27c779164f4fa0c75897a6e95b35f820a2a10e7c244b8923c575e0ea46f15f6b" | ||
| license "GPL-3.0-only" | ||
| head "https://github.com/citiususc/veryfasttree.git", branch: "master" | ||
|
|
||
| bottle do | ||
| sha256 cellar: :any, arm64_sequoia: "be966294bd7e7793920e064538c8f301d30cf36e836149151a7dc9749751699e" | ||
| sha256 cellar: :any, arm64_sonoma: "ad4a872d4517fad3f3a1ee924c42cd529cc50583d1cd01267808a64f30122c33" | ||
| sha256 cellar: :any, arm64_ventura: "5feeb83511115643cddc8bd05cea9b8215606d1e39edb9eba23028c5d646a02e" | ||
| sha256 cellar: :any, sonoma: "84f8d609b53f4eccf0471604f90098e8a2e9525cc1eb8a942a0a9896f405bcf5" | ||
| sha256 cellar: :any, ventura: "b675c4443158d46942e000086a79e1b3d8262ffb9703d9dd23ae256fea2895d8" | ||
| sha256 cellar: :any_skip_relocation, x86_64_linux: "93bc3678c5bc47c3f3a82b01e6a81ce7c247119fa1086cd1c5c1bafa4f979720" | ||
| end | ||
|
|
||
| depends_on "boost" => :build | ||
| depends_on "cmake" => :build | ||
| depends_on "robin-map" => :build | ||
| depends_on "xxhash" => :build | ||
| depends_on "libomp" | ||
| uses_from_macos "bzip2" | ||
| uses_from_macos "zlib" | ||
|
|
||
| fails_with :gcc do | ||
| version "4" # fails with GCC 4.x and earlier | ||
| cause "Requires gcc >=5" | ||
| end | ||
|
|
||
| def install | ||
| system "cmake", "-S", ".", "-B", "build", "-DUSE_SHARED=ON", "-DUSE_NATIVE=OFF", *std_cmake_args | ||
| system "cmake", "--build", "build" | ||
| system "cmake", "--install", "build" | ||
| man1.install "man/VeryFastTree.1" | ||
| end | ||
|
|
||
| test do | ||
| (testpath/"test.fasta").write <<~EOS | ||
| >N3289 | ||
| --RNRSCRRDNTNGQDLQAALAIFAAKVYVGVALQSVQVAAGIGKHPVYKHIPSKKYTGL | ||
| IIQELYLERLMAELADGLADAAPDVLLDIRGLMLALDAPAREKPIIL-LHLAASAGDALR | ||
| DKGQALRRELLPRLSGLGYAGLASGALTGDNATLMSARLIGLLVSATLLAL--------- | ||
| ----------------- | ||
| >N1763 | ||
| ------ISKDTTEERFLEVDKLTFAPKSYAGTLQTKILSAVSVPAGTLYKDFPTTELALL | ||
| VTLEVYQATDTSGAQDGLAANARDILHVLVELFLALAGFAAQDPLHLLLPMAAALTSSLR | ||
| GRLRELRRELLAKGAAKVYTGLGAADATGDGVQLGAASLAMQLLGALLPCLRLDALLGSL | ||
| ASGLPEEKLASLAIFL- | ||
| >N2100 | ||
| --RGRARPKQTTAESNLDATMGKFASQEYDGTMHRELGAASGVSLGTLYPDYPTWEMLIL | ||
| VTLESYLEPVVSALYAGLATDAPDILQR-LQLFLALLGFAMNHPGALLKSLAATLESELC | ||
| GKLKALTREVLEKLGASVFEGLPEPTLTGDEATPMSAALLMPLVQALLLCLLLQPLLAKH | ||
| SDDLPQIILAIYGIF-- | ||
| >N774 | ||
| --RGRRRTKTIVSEKDLSATMGRFAEQPYDGSLERNAATAASAPLNTMYGEFPTQDMFLL | ||
| MCLESYLIPTVLEADAE-ATEARDVLRRRLQLFLALLGFALNHPTQLLKMLATTLHKALR | ||
| GKIKDLQREVFARLTASAPAGLAAQFLTGDNATLMEAVLLMPFLAALLSCLILEPLDRKF | ||
| ADDFPAVILAIYAIF-- | ||
| >N211 | ||
| --KARGRTTIETGEKVLTGEMDRFAELQYDGSLQRDDTTGAAPPLGTLYGKLPTQDMFLL | ||
| FALESYLDPGTPELGQGLATKAPDGLRKRLHLFLGLLSFSLDHPVHLLKSLATT-HKAVR | ||
| GKVKDLQRDRFARLNASAPSGIAHPALTGDMATLMEAGLLMPLLAALLPILILAPLDKKY | ||
| AHDNHNDILAIYAIFLT | ||
| >N747 | ||
| MGKARGITTAYAYSQVLIGRLGAHAALPYNGSLERKDVAALDAPTNKLYGQFPDGDSWLL | ||
| GALEAYIHTCPPELPQSLATQAPETIFTRLQPYLGLADFGLAHPGQLLKIEATKLQRAVR | ||
| GKFKELQKDAPAQLTANGITVVGQPNLTGDLGTLSEAVVLLQLVPSLLAAIIFKPIDKKY | ||
| GESAPVGILLPFSVW-- | ||
| >N952 | ||
| MGRGRARTTVEAGEKVLLGTMIRFAELPHDGSLQRNDSTALAAPLNTLYAKFPTQDMFLL | ||
| FALESYLHPSSPELGMGLATPAPDILRKRLALFLGLLSFSLEHPIQLLKSLATT-HKAVR | ||
| GPFKDLQKDVPAHLTATAPSGIAHPALTGDMATLMEAVLLMPLLAALLPVLVLKPLDKKF | ||
| ADDSPGDILAVYAIF-- | ||
| >N3964 | ||
| ------RTTVEDNDKVLNATMDRFADLPYDGSLQRDDTTAQTAPLGTLYGKFPTADMFLL | ||
| NALESYLDPKRPELGQGLATKAPDALRKKLQLFLGLLAFALSHPNRLLKSLATT-HKLVR | ||
| GKLKDQEREIFARLTASAPPAIAHPALTGDMATLMEAVLLMPLLAALLTVLPLEPLDKAY | ||
| EDDSPGDILAVYAVF-- | ||
| >N3613 | ||
| LGRGMARTTVEDLETVLNATMDRFAQLPYDGSLQRDDTTAASAPLGTLYGKSPTADMFLQ | ||
| FALESYLDPKRPELGQGLATKAPDALRKRLQLYLGLLSFALEHPTPLLQSLATTLHK-VR | ||
| GKLKNLQREVFARLTASAASGIAHPALTGDMATLMDAVLLMPLLAKLLTIIILEPLDKKY | ||
| SDNSPDDILAAYAAFLS | ||
| >N1689 | ||
| MKLGRYRTVQTANEKYLETTAGRYADQNYAGTAQRGVQKANSVPLGTLYPDLPTRDMLLL | ||
| VSLESYLESITAGL-AGLATKAVTLFKVVLVLFLSVTGFALSHPGELFLSMAAVLQTEIR | ||
| GKLKNLTRELLQKLSASLTAGLAVPELTGDEASLGAGKILVPLLAALLVALLLSPLLGGF | ||
| SDDLPNMVLAIYAVTL- | ||
| >N3700 | ||
| MKMGRPRTKQSTSQRYLDTAGARYDDQAYAGTLQRGLGNAKGVPLGTLYLDFPIRDMLLL | ||
| VTLESYLESIVAGLYA-GATKAPNLLQAVLILFLNVVGFALLHPGALLLTMAAVLHNELI | ||
| GKLKEFSRELLERLAASVITGLAVPELTGDEGTLAAGVILMALLAALLLYLLLDPLLSGF | ||
| SGDLPDSGLAVHA---- | ||
| EOS | ||
| system bin/"VeryFastTree", "test.fasta" | ||
| end | ||
| end |