From 10a044bc34a4112c17edcfd4c9e057ec49b806d6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?C=C3=A9sar=20Pomar?= <cesarpomar18@gmail.com>
Date: Fri, 20 Sep 2024 01:39:43 +0200
Subject: [PATCH] veryfasttree 4.0.4 (new formula)

Co-authored-by: Carlo Cabrera <30379873+carlocab@users.noreply.github.com>
---
 Formula/v/veryfasttree.rb | 89 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 89 insertions(+)
 create mode 100644 Formula/v/veryfasttree.rb

diff --git a/Formula/v/veryfasttree.rb b/Formula/v/veryfasttree.rb
new file mode 100644
index 000000000000..b791ceb1e087
--- /dev/null
+++ b/Formula/v/veryfasttree.rb
@@ -0,0 +1,89 @@
+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"
+
+  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