class Blast < Formula
  desc "Basic Local Alignment Search Tool"
  homepage "https://blast.ncbi.nlm.nih.gov/"
  url "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.7.1+-src.tar.gz"
  version "2.7.1"
  sha256 "10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca"

  bottle do
    rebuild 1
    sha256 "1f0bdc5f64acf3ce913b36c3531ca631669bd2afbf5eaf8aa66d94432d497a31" => :mojave
    sha256 "18545f187e9af022d46e20bccbf4666c0d89033c7a3fe471174dc9bfda4abf94" => :high_sierra
    sha256 "243c089a32cce6871b3ca55da06749257e1de2cec3c8b46301b09a5135776711" => :sierra
  end

  depends_on "lmdb"

  conflicts_with "proj", :because => "both install a `libproj.a` library"

  def install
    cd "c++" do
      # Use ./configure --without-boost to fix
      # error: allocating an object of abstract class type 'ncbi::CNcbiBoostLogger'
      # Boost is used only for unit tests.
      # See https://github.com/Homebrew/homebrew-science/pull/3537#issuecomment-220136266
      system "./configure", "--prefix=#{prefix}",
                            "--without-debug",
                            "--without-boost"

      # Fix the error: install: ReleaseMT/lib/*.*: No such file or directory
      system "make"

      system "make", "install"
    end
  end

  test do
    (testpath/"test.fasta").write <<~EOS
      >U00096.2:1-70
      AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
    EOS
    output = shell_output("#{bin}/blastn -query test.fasta -subject test.fasta")
    assert_match "Identities = 70/70", output
  end
end