class Abyss < Formula
  desc "Genome sequence assembler for short reads"
  homepage "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
  url "https://github.com/bcgsc/abyss/releases/download/2.1.5/abyss-2.1.5.tar.gz"
  sha256 "65bfc8241e6ff5adf7601ae4ae93a75e3db86d6bff5d593c75aaff7f0ef41757"

  bottle do
    cellar :any
    sha256 "9899d03cf2714ffc25adcac83e4b424c03022b6896c3112f49d01f585b0d3a7c" => :mojave
    sha256 "3c358f580990e5edb642524dc83d7cf82cff1788649ef2584dd8e9113d9f7821" => :high_sierra
    sha256 "56097dc4da0f6700dface6d4a36b5064b3401f2ba7b874cc61736f4a06047cdf" => :sierra
  end

  head do
    url "https://github.com/bcgsc/abyss.git"

    depends_on "autoconf" => :build
    depends_on "automake" => :build
    depends_on "multimarkdown" => :build
  end

  depends_on "boost" => :build
  depends_on "google-sparsehash" => :build
  depends_on "gcc"
  depends_on "open-mpi"

  fails_with :clang # no OpenMP support

  resource("testdata") do
    url "http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz"
    sha256 "28f8592203daf2d7c3b90887f9344ea54fda39451464a306ef0226224e5f4f0e"
  end

  def install
    system "./autogen.sh" if build.head?
    system "./configure", "--enable-maxk=128",
                          "--prefix=#{prefix}",
                          "--with-boost=#{Formula["boost"].include}",
                          "--with-mpi=#{Formula["open-mpi"].prefix}",
                          "--with-sparsehash=#{Formula["google-sparsehash"].prefix}",
                          "--disable-dependency-tracking",
                          "--disable-silent-rules"
    system "make", "install"
  end

  test do
    testpath.install resource("testdata")
    system "#{bin}/abyss-pe", "k=25", "name=ts", "in=reads1.fastq reads2.fastq"
    system "#{bin}/abyss-fac", "ts-unitigs.fa"
  end
end