diff --git a/Formula/v/veryfasttree.rb b/Formula/v/veryfasttree.rb new file mode 100644 index 000000000000..2ae2304c78c3 --- /dev/null +++ b/Formula/v/veryfasttree.rb @@ -0,0 +1,98 @@ +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