<commit_before>class TCoffee < Formula
  homepage "http://www.tcoffee.org/"
  version '9.03.r1336'
  url "http://www.tcoffee.org/Packages/Beta/Version_9.03.r1336/T-COFFEE_distribution_Version_9.03.r1336.tar.gz"
  sha256 "02147aa10c033b75658e360dc45ed1deaca4b6edc4c95b8bedde169e69568aac"
  # doi "10.1006/jmbi.2000.4042"

  depends_on 'poa'
  depends_on 'dalign-tx'
  depends_on 'dalign'
  depends_on 'pcma'
  depends_on 'probcons'
  depends_on 'clustal-w'
  depends_on 'mafft'
  depends_on 'muscle'

  def install
    cd 't_coffee_source' do
      system *%w[make t_coffee]
      bin.install 't_coffee'
      #prefix.install "lib" => "libexec"
      #prefix.install Dir["*"]
      #bin.install_symlink "../compile/t_coffee"
    end
    prefix.install 'mcoffee'
  end

  test do
    system "#{bin}/t_coffee -version"
  end
end<commit_msg>Adding a bash file env<commit_after>class TCoffee < Formula
  homepage "http://www.tcoffee.org/"
  version '9.03.r1336'
  url "http://www.tcoffee.org/Packages/Beta/Version_9.03.r1336/T-COFFEE_distribution_Version_9.03.r1336.tar.gz"
  sha256 "02147aa10c033b75658e360dc45ed1deaca4b6edc4c95b8bedde169e69568aac"
  # doi "10.1006/jmbi.2000.4042"

  depends_on 'poa'
  depends_on 'dialign-tx'
  depends_on 'dialign-t'
  depends_on 'pcma'
  depends_on 'probcons'
  depends_on 'clustal-w'
  depends_on 'mafft'
  depends_on 'muscle'

  def install
    cd 't_coffee_source' do
      system *%w[make t_coffee]
      bin.install 't_coffee'
      #prefix.install "lib" => "libexec"
      #prefix.install Dir["*"]
      #bin.install_symlink "../compile/t_coffee"
    end
    (prefix+'plugins').install 'mcoffee'
    File.open((etc+'tcoffee.bash'), 'w') { |file| file.write("export MCOFFEE_4_TCOFFEE=#{prefix}/plugins/mcoffee\n") }
  end

  test do
    system "#{bin}/t_coffee -version"
  end
end
{'fraction_non_alphanumeric': 0.132013201320132, 'fraction_numerical': 0.08085808580858085, 'mean_word_length': 3.724675324675325, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 4, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6145212', 'n_tokens_mistral': 871, 'n_tokens_neox': 767, 'n_words': 122}