beast.rb

class Beast < Formula
  desc "Bayesian Evolutionary Analysis Sampling Trees"
  homepage "http://beast.bio.ed.ac.uk/"
  # doi "10.1093/molbev/mss075"
  # tag "bioinformatics"

  url "http://tree.bio.ed.ac.uk/download.php?id=92&num=3"
  version "1.8.2"
  sha256 "233ca5e06d98c5e7f8fb6a68fe5dd5448bb36d7d801117f7f6f11ac9f6b6ecc9"

  bottle do
    cellar :any
    sha256 "e1357fad70b3a51ce734a705667f2e9d16bdddf480bf340559cdad0bbcaacb65" => :yosemite
    sha256 "c411831dc26441e4b5bd92dc1926fbd8171d5c8d26d17239f2ce1e9604f67f8b" => :mavericks
    sha256 "c3974c08c01dfa26db9407b070b4302a109043725fef586b4d82290603f2dfee" => :mountain_lion
  end

  head do
    url "https://github.com/beast-dev/beast-mcmc.git"
    depends_on :ant
  end

  def install
    system "ant", "linux" if build.head?

    # Move jars to libexec
    inreplace Dir["bin/*"] do |s|
      s["$BEAST/lib"] = "$BEAST/libexec"
    end

    mv "lib", "libexec"
    prefix.install Dir[build.head? ? "release/Linux/BEASTv*/*" : "*"]
  end

  def caveats; <<-EOS.undent
    Examples are installed in:
      #{opt_prefix}/examples/
    EOS
  end

  test do
    system "#{bin}/beast", "-help"
  end
end