class Kaiju < Formula
  # Menzel_2016: "https://doi.org/10.1038/ncomms11257"
  desc "Fast taxonomic classification of metagenomic sequencing reads"
  homepage "https://kaiju.binf.ku.dk/"
  url "https://github.com/bioinformatics-centre/kaiju/archive/refs/tags/v1.9.2.tar.gz"
  sha256 "58d922358dfa4a608be888ec5c9e615b45b1e4be50615429183b0c5355e89c78"
  license "GPL-3.0-only"

  bottle do
    root_url "https://ghcr.io/v2/brewsci/bio"
    sha256 cellar: :any_skip_relocation, monterey:     "544fe33129ffc09e488eecc1a70ecf69b1d1f477d6692d2fa9cbf98b1f0b1558"
    sha256 cellar: :any_skip_relocation, x86_64_linux: "f0308b0f34baa5d661c80ef1affeba2a2b89bdde06acf4f088524959ff71a284"
  end

  uses_from_macos "perl"
  uses_from_macos "zlib"

  def install
    system "make", "-C", "src"

    # https://github.com/bioinformatics-centre/kaiju/issues/93
    inreplace "bin/kaiju-makedb" do |s|
      s.gsub! "$SCRIPTDIR/kaiju-convertMAR.py", pkgshare/"kaiju-convertMAR.py"
      s.gsub! "$SCRIPTDIR/kaiju-taxonlistEuk.tsv", pkgshare/"kaiju-taxonlistEuk.tsv"
      s.gsub! "$SCRIPTDIR/kaiju-excluded-accessions.txt", pkgshare/"kaiju-excluded-accessions.txt"
    end

    pkgshare.install "bin/kaiju-convertMAR.py"
    pkgshare.install "bin/kaiju-taxonlistEuk.tsv"
    pkgshare.install "bin/kaiju-excluded-accessions.txt"

    bin.install Dir["bin/*"]
  end

  def caveats
    <<~EOS
      You must build a #{name} database before usage.
      See #{opt_prefix}/README.md for details.
    EOS
  end

  test do
    assert_match version.to_s, shell_output("#{bin}/kaiju -h 2>&1", 1)
  end
end