<commit_before>class Bowtie2 < Formula
  desc "A fast and sensitive gapped read aligner"
  homepage "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml"
  # doi "10.1038/nmeth.1923"
  # tag "bioinformatics"
  head "https://github.com/BenLangmead/bowtie2.git"
  url "https://github.com/BenLangmead/bowtie2/archive/v2.2.6.tar.gz"
  sha256 "fb4d09a96700cc929e8191659ee8509bb2f19816235322d1f012338d4a177358"

  bottle do
    cellar :any
    revision 1
    sha256 "228edcb384d3854fe3954fcfdd3856470be97356c92787ad7931aa9bf1b705d0" => :yosemite
    sha256 "34b8f416f4761fbcbde9b6336a41f20be02bb7cef86fbf968379f28f8d6a178f" => :mavericks
    sha256 "6b775646d6b84ff565536b10ae3ce7b3ab47a2c935f8120bc31a2cdf8d77c8ea" => :mountain_lion
  end

  depends_on "tbb"

  def install
    system "make", "install", "WITH_TBB=1", "prefix=#{prefix}"
    pkgshare.install "example", "scripts"
  end
<commit_msg>bowtie2: configurable TBB support<commit_after>class Bowtie2 < Formula
  desc "A fast and sensitive gapped read aligner"
  homepage "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml"
  # doi "10.1038/nmeth.1923"
  # tag "bioinformatics"
  head "https://github.com/BenLangmead/bowtie2.git"
  url "https://github.com/BenLangmead/bowtie2/archive/v2.2.6.tar.gz"
  sha256 "fb4d09a96700cc929e8191659ee8509bb2f19816235322d1f012338d4a177358"

  bottle do
    cellar :any
    revision 1
    sha256 "228edcb384d3854fe3954fcfdd3856470be97356c92787ad7931aa9bf1b705d0" => :yosemite
    sha256 "34b8f416f4761fbcbde9b6336a41f20be02bb7cef86fbf968379f28f8d6a178f" => :mavericks
    sha256 "6b775646d6b84ff565536b10ae3ce7b3ab47a2c935f8120bc31a2cdf8d77c8ea" => :mountain_lion
  end

  option "without-tbb", "Build without using Intel Thread Building Blocks (TBB)"

  if build.with? "tbb"
    depends_on "tbb"
  end

  def install
    if build.with? "tbb"
      system "make", "install", "WITH_TBB=1",
             "EXTRA_FLAGS=-L #{HOMEBREW_PREFIX}/lib",
             "INC=-I #{HOMEBREW_PREFIX}/include", "prefix=#{prefix}"
    else
      system "make", "install", "prefix=#{prefix}"
    end
    pkgshare.install "example", "scripts"
  end

{'fraction_non_alphanumeric': 0.1080188679245283, 'fraction_numerical': 0.18443396226415093, 'mean_word_length': 4.625994694960212, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 9, 'https://': 4, 'lorem ipsum': 0, 'www.': 0, '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': '2578517', 'n_tokens_mistral': 1111, 'n_tokens_neox': 899, 'n_words': 134}