class Bowtie2 < Formula
  desc "Fast and sensitive gapped read aligner"
  homepage "https://bowtie-bio.sourceforge.io/"
  url "https://github.com/BenLangmead/bowtie2/archive/v2.3.3.tar.gz"
  sha256 "7d4d455a4af70d02a1ae4ce1a0b21b7d3018737dd197579e1a5612a5c01887c8"

  depends_on "tbb"

  def install
    tbb = Formula["tbb"]
    system "make", "install", "WITH_TBB=1", "prefix=#{prefix}",
           "EXTRA_FLAGS=-L #{tbb.opt_lib}", "INC=-I #{tbb.opt_include}"

    pkgshare.install "example", "scripts"
  end

  test do
    system "#{bin}/bowtie2-build",
           "#{pkgshare}/example/reference/lambda_virus.fa", "lambda_virus"
    assert_predicate testpath/"lambda_virus.1.bt2", :exist?,
                     "Failed to create viral alignment lambda_virus.1.bt2"
  end
end