class Abyss < Formula
  desc "Genome sequence assembler for short reads"
  homepage "https://www.bcgsc.ca/resources/gsc-software-centre"
  url "https://github.com/bcgsc/abyss/releases/download/2.2.3/abyss-2.2.3.tar.gz"
  sha256 "ac7679ececbdd89cc050998eae31fa5f8bf7cdab6a0c05eb5eb1e3867c7e75cb"

  bottle do
    cellar :any
    sha256 "fe5e65727d390f31e0e847e30da9a6b931c7b1b5f3c0a4e6459b5aa0f4eb0ad9" => :catalina
    sha256 "d982f22bbc71a21271eb01441f4189366e91bfb3dc8c9718df09307eb89bf11e" => :mojave
    sha256 "482a9754933a932ca3d8860de7f753b72a1a344ddaf40104849ba999218d86a8" => :high_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 "https://www.bcgsc.ca/sites/default/files/bioinformatics/software/abyss/releases/1.3.4/test-data.tar.gz"
    sha256 "28f8592203daf2d7c3b90887f9344ea54fda39451464a306ef0226224e5f4f0e"
  end

  def install
    ENV.delete("HOMEBREW_SDKROOT") if MacOS.version >= :mojave && MacOS::CLT.installed?
    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