class Kallisto < Formula
  desc "Quantify abundances of transcripts from RNA-Seq data"
  homepage "https://pachterlab.github.io/kallisto/"
  url "https://github.com/pachterlab/kallisto/archive/v0.45.1.tar.gz"
  sha256 "2c97280c69991f995f77e7c8ab56ae5060329c90f7f0d7e9ca2f01dd50ee378f"

  bottle do
    cellar :any
    sha256 "60b4b2ac31be396caaf7a07d403be9572451fe1583f638e1e3782c99cc66973b" => :mojave
    sha256 "265a37e38c894f343a1f245c7c0b1147788bdc294dae5c765e6e7c4edb86bccd" => :high_sierra
    sha256 "67d589175fc046e782a761597c3a5d11623770cc9937939eadeff3f535f04dd4" => :sierra
  end

  depends_on "autoconf" => :build
  depends_on "automake" => :build
  depends_on "cmake" => :build
  depends_on "hdf5"

  def install
    # Upstream issue 15 Feb 2018 "cmake does not run autoreconf for htslib"
    # https://github.com/pachterlab/kallisto/issues/159
    system "autoreconf", "-fiv", "ext/htslib"

    system "cmake", ".", *std_cmake_args

    # Upstream issue 15 Feb 2018 "parallelized build failure"
    # https://github.com/pachterlab/kallisto/issues/160
    # Upstream issue 15 Feb 2018 "cannot use system htslib"
    # https://github.com/pachterlab/kallisto/issues/161
    system "make", "htslib"

    system "make", "install"
  end

  test do
    (testpath/"test.fasta").write <<~EOS
      >seq0
      FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF
    EOS
    output = shell_output("#{bin}/kallisto index -i test.index test.fasta 2>&1")
    assert_match "has 1 contigs and contains 32 k-mers", output
  end
end