velvet.rb

require 'formula'

class Velvet < Formula
  homepage 'http://www.ebi.ac.uk/~zerbino/velvet/'
  url 'http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz'
  sha1 '216f0941609abf3a73adbba19ef1f364df489d18'

  head 'https://github.com/dzerbino/velvet.git'

  option 'with-maxkmerlength=', 'Specify maximum k-mer length, any positive odd integer (default: 31)'
  option 'with-categories=', 'Specify number of categories, any positive integer (default: 2)'

  def install
    args = ["CFLAGS=-Wall -m64", "LONGSEQUENCES=1"]
    args << "OPENMP=1" unless ENV.compiler == :clang
    maxkmerlength = ARGV.value('with-maxkmerlength') || '-1'
    categories = ARGV.value('with-categories') || '-1'
    args << "MAXKMERLENGTH=#{maxkmerlength}" if maxkmerlength.to_i > 0
    args << "CATEGORIES=#{categories}" if categories.to_i > 0

    system "make", "velveth", "velvetg", *args
    bin.install 'velveth', 'velvetg'

    # install additional contributed scripts
    (share / 'velvet/contrib').install Dir['contrib/shuffleSequences_fasta/shuffleSequences_*']
  end

  def caveats
    <<-EOS.undent
      Some additional user contributed scripts are installed here:
      #{share}/velvet/contrib
    EOS
  end

  def test
    system "velveth --help"
    system "velvetg --help"
  end
end