class Diamond < Formula
  desc "Accelerated BLAST compatible local sequence aligner"
  homepage "https://www.wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/diamond/"
  url "https://github.com/bbuchfink/diamond/archive/v2.0.7.tar.gz"
  sha256 "ece969b38620e3540e8510496212149030a9918bd32f7f68aee628b788acb3e6"
  license "GPL-3.0-or-later"

  bottle do
    sha256 cellar: :any_skip_relocation, arm64_big_sur: "c573e096c0fc3f51cca1d01b8ed844a72e32363c84b4288e870f8532bf621593"
    sha256 cellar: :any_skip_relocation, big_sur:       "5d347c31e0e69187454084656a564d4d6a21201efa4420084b058157d2059407"
    sha256 cellar: :any_skip_relocation, catalina:      "4b23cf7459b30d36c07f9d22664eab2b9966bd720a687435fae99ac1e849f640"
    sha256 cellar: :any_skip_relocation, mojave:        "d1bbd8ebcaf859efd57d6ab9fd9ccb6187e44771baf3fc728026e30320e58f71"
  end

  depends_on "cmake" => :build

  uses_from_macos "zlib"

  def install
    system "cmake", ".", *std_cmake_args
    system "make", "install"
  end

  test do
    (testpath/"nr.faa").write <<~EOS
      >gnl|alu|HSU14568_Alu_Sb_consensus_rf1
      grarwltpvipalweaeaggsrgqeietilantvkprlyXkyknXpgvvagacspsysgg
      XgrrmaXtreaelavsrdratalqpgrqsetpsqkk
      >gnl|alu|HSU14568_Alu_Sb_consensus_rf2
      agrggsrlXsqhfgrprradhevrrsrpswltrXnpvstkntkisrawwrapvvpatrea
      eagewrepgrrslqXaeiaplhsslgdrarlrlkk
      >gnl|alu|HSU14568_Alu_Sb_consensus_rf3
      pgavahacnpstlggrggritrsgdrdhpgXhgetpsllkiqklagrgggrlXsqllgrl
      rqengvnpgggacseprsrhctpawaterdsvskk
      >gnl|alu|HSU14568_Alu_Sb_consensus_rf-1
      fflrrslalsprlecsgaisahcklrlpgsrhspasasrvagttgarhharlifvflvet
      gfhrvsqdgldlltsXsarlglpkcwdyrrepprpa
      >gnl|alu|HSU14568_Alu_Sb_consensus_rf-2
      ffXdgvslcrpgwsavarsrltassasrvhaillpqppeXlglqapattpgXflyfXXrr
      gftvlarmvsisXprdppasasqsagitgvshrar
      >gnl|alu|HSU14568_Alu_Sb_consensus_rf-3
      ffetesrsvaqagvqwrdlgslqapppgftpfsclslpsswdyrrppprpanfcifsrdg
      vspcXpgwsrspdlvirpprppkvlglqaXatapg
    EOS
    output = shell_output("#{bin}/diamond makedb --in nr.faa -d nr 2>&1")
    assert_match "Processed 6 sequences, 572 letters.", output
  end
end