class Mmseqs2 < Formula
  desc "Software suite for very fast protein sequence search and clustering"
  homepage "https://mmseqs.org/"
  url "https://github.com/soedinglab/MMseqs2/archive/3-be8f6.tar.gz"
  version "3-be8f6"
  sha256 "7502adcec9f84c560996ced29edec88ce8ec47670da7dae6c7ee50d7b849fe0d"

  bottle do
    cellar :any
    sha256 "0a2bc5f422c1fba52f2e20e3c27559c086bd4f1a652739c32840a730bbcac30e" => :high_sierra
    sha256 "3e0fb89409e53fbef476d40296f35cae6d36018691eb0f72278affb4b8154f23" => :sierra
    sha256 "ecb8fba6928eaf995c8176dcdb44cf13adc0a823b4183ecfe633faf57cc9520c" => :el_capitan
  end

  depends_on "cmake" => :build
  depends_on "gcc"

  cxxstdlib_check :skip

  fails_with :clang # needs OpenMP support

  resource "documentation" do
    url "https://github.com/soedinglab/MMseqs2.wiki.git",
        :revision => "f6b31176d50402ce6070c9557a476e06a872d2ae"
  end

  def install
    args = *std_cmake_args << "-DHAVE_TESTS=0" << "-DHAVE_MPI=0"
    args << "-DVERSION_OVERRIDE=#{version}"

    args << "-DHAVE_SSE4_1=1" if build.bottle?

    system "cmake", ".", *args
    system "make", "install"

    resource("documentation").stage { doc.install Dir["*"] }
    pkgshare.install "examples"
    bash_completion.install "util/bash-completion.sh" => "mmseqs.sh"
  end

  def caveats
    unless Hardware::CPU.sse4?
      "MMseqs2 requires at least SSE4.1 CPU instruction support. The binary will not work correctly."
    end
  end

  test do
    system "#{bin}/mmseqs", "createdb", "#{pkgshare}/examples/QUERY.fasta", "q"
    system "#{bin}/mmseqs", "cluster", "q", "res", "tmp", "-s", "1"
    assert_predicate testpath/"res", :exist?
    assert_predicate (testpath/"res").size, :positive?
    assert_predicate testpath/"res.index", :exist?
    assert_predicate (testpath/"res.index").size, :positive?
  end
end