augustus.rb

class Augustus < Formula
  desc "predict genes in eukaryotic genomic sequences"
  homepage "http://bioinf.uni-greifswald.de/augustus/"
  # doi "10.1093/nar/gkh379"
  # tag "bioinformatics"

  url "http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.2.tar.gz"
  sha256 "bb36fcaaaab32920908e794d04e6cb57a0c61d689bfbd31b9b6315233ea3559e"
  revision 4

  bottle do
    sha256 "decae226649599fa6269282d03126385061900894053c553edb6f263b3c35042" => :sierra
    sha256 "a7e9b87f9d434109560fd6868565858bbcc9e9d2fd96323b10ed26688f808a09" => :el_capitan
    sha256 "ed8bb0c941c364accd58572817678a4b330a9b5f0211f9fbc2f8ebd3a6cdfe38" => :x86_64_linux
  end

  option "with-cgp",  "Enable comparative gene prediction"

  depends_on "bamtools"
  depends_on "boost"

  if build.with? "cgp"
    depends_on "gsl"
    depends_on "lp_solve"
    depends_on "suite-sparse"
  end

  def install
    args = []
    args << "COMPGENEPRED=true" if build.with? "cgp"

    system "make", "-C", "auxprogs/filterBam/src", "BAMTOOLS=#{Formula["bamtools"].opt_include}/bamtools", *args
    system "make", "INCLUDES=#{Formula["bamtools"].opt_include}/bamtools", *args

    rm_r %w[include src]
    libexec.install Dir["*"]
    bin.install_symlink Dir[libexec/"bin/*"]
  end

  def caveats; <<-EOS.undent
    Set the environment variable AUGUSTUS_CONFIG_PATH:
      export AUGUSTUS_CONFIG_PATH=#{opt_prefix}/libexec/config
    EOS
  end

  test do
    system "#{bin}/augustus", "--version"
  end
end