<commit_before>require 'formula'

class Maker < Formula
  homepage 'http://www.yandell-lab.org/software/maker.html'
  #doi '10.1101/gr.6743907' => 'MAKER', '10.1104/pp.113.230144' => 'MAKER-P'
  url 'http://yandell.topaz.genetics.utah.edu/maker_downloads/static/maker-2.31.tgz'
  sha1 'b90176010de9fcaf643c988e6c78b311a445ceab'

  depends_on 'augustus' => :recommended
  depends_on 'blast'
  depends_on 'exonerate'
  depends_on 'infernal' => :optional
  depends_on :mpi => :optional
  depends_on 'repeatmasker'
  depends_on 'snap'
  depends_on 'trnascan' => :optional
  # No formula: depends_on 'genemark-es' => :optional
  # No formula: depends_on 'genemarks' => :optional

  depends_on 'Bio::Perl' => :perl
  depends_on 'Bit::Vector' => :perl
  depends_on 'DBD::SQLite' => :perl
  depends_on 'DBI' => :perl
  depends_on 'File::Which' => :perl
  depends_on 'IO::All' => :perl
  depends_on 'IO::Prompt' => :perl
  depends_on 'Inline' => :perl
  depends_on 'Perl::Unsafe::Signals' => :perl
  depends_on 'PerlIO::gzip' => :perl
  depends_on 'forks' => :perl
  depends_on 'forks::shared' => :perl

  def install
    cd 'src' do
      system 'yes "" |perl Build.PL'
      system *%w[./Build install]
    end
    libexec.install Dir['*']
    bin.install_symlink %w[
      ../libexec/bin/gff3_merge
      ../libexec/bin/maker]
  end

  def caveats; <<-EOS.undent
    Optional components of MAKER
    1. Augustus 2.0 or higher. Download from http://bioinf.uni-greifswald.de/augustus/
    2. GeneMark-ES. Download from http://exon.biology.gatech.edu
    3. FGENESH 2.4 or higher. Purchase from http://www.softberry.com
    4. GeneMarkS. Download from http://exon.biology.gatech.edu
    EOS
  end

  test do
    system 'maker --version'
  end
end
<commit_msg>maker 2.31.3<commit_after>require 'formula'

class Maker < Formula
  homepage 'http://www.yandell-lab.org/software/maker.html'
  #doi '10.1101/gr.6743907' => 'MAKER', '10.1104/pp.113.230144' => 'MAKER-P'
  url 'http://yandell.topaz.genetics.utah.edu/maker_downloads/static/maker-2.31.3.tgz'
  sha1 'f9e8645e859f648badacdb243cf097305c3e95c7'

  depends_on 'augustus' => :recommended
  depends_on 'blast'
  depends_on 'exonerate'
  depends_on 'infernal' => :optional
  depends_on :mpi => :optional
  depends_on 'repeatmasker'
  depends_on 'snap'
  depends_on 'trnascan' => :optional
  # No formula: depends_on 'genemark-es' => :optional
  # No formula: depends_on 'genemarks' => :optional

  depends_on 'Bio::Perl' => :perl
  depends_on 'Bit::Vector' => :perl
  depends_on 'DBD::SQLite' => :perl
  depends_on 'DBI' => :perl
  depends_on 'File::Which' => :perl
  depends_on 'IO::All' => :perl
  depends_on 'IO::Prompt' => :perl
  depends_on 'Inline' => :perl
  depends_on 'Perl::Unsafe::Signals' => :perl
  depends_on 'PerlIO::gzip' => :perl
  depends_on 'forks' => :perl
  depends_on 'forks::shared' => :perl

  def install
    cd 'src' do
      system 'yes "" |perl Build.PL'
      system *%w[./Build install]
    end
    libexec.install Dir['*']
    bin.install_symlink %w[
      ../libexec/bin/gff3_merge
      ../libexec/bin/maker]
  end

  def caveats; <<-EOS.undent
    Optional components of MAKER
    1. Augustus 2.0 or higher. Download from http://bioinf.uni-greifswald.de/augustus/
    2. GeneMark-ES. Download from http://exon.biology.gatech.edu
    3. FGENESH 2.4 or higher. Purchase from http://www.softberry.com
    4. GeneMarkS. Download from http://exon.biology.gatech.edu
    EOS
  end

  test do
    system 'maker --version'
  end
end

{'fraction_non_alphanumeric': 0.14767209368751785, 'fraction_numerical': 0.038560411311053984, 'mean_word_length': 3.507078507078507, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 43, 'https://': 0, 'lorem ipsum': 0, 'www.': 4, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 8, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5404078', 'n_tokens_mistral': 1466, 'n_tokens_neox': 1372, 'n_words': 289}