<commit_before>class Cufflinks < Formula
  homepage "http://cufflinks.cbcb.umd.edu/"
  url "http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.tar.gz"
  sha256 "e8316b66177914f14b3a0c317e436d386a46c4c212ca1b2326f89f8a2e08d5ae"

  bottle do
    root_url "https://homebrew.bintray.com/bottles-science"
    cellar :any
    sha256 "68750a99e5cf104666cfc068c4bfddf8c2aebe2cb44bf5360aac2b5f4e181000" => :yosemite
    sha256 "3313084062765bee932d05d0bc8477887ec6a61e788c9a465c907cc363b44370" => :mavericks
    sha256 "d1e789b72fe73af8cb46aa71feeedea398df2c4b1e9fce5604492a7945143487" => :mountain_lion
  end

  depends_on "homebrew/versions/boost155" => :build
  depends_on "samtools-0.1"
  depends_on "eigen"

  def install
    ENV["EIGEN_CPPFLAGS"] = "-I#{Formula["eigen"].opt_include}/eigen3"
    ENV.append "LIBS", "-lboost_system-mt -lboost_thread-mt -lboost_serialization-mt"
    system "./configure", "--disable-debug",
                          "--disable-dependency-tracking",
                          "--prefix=#{prefix}",
                          "--mandir=#{man}"
    system "make"
    ENV.j1
    system "make", "install"
  end<commit_msg>cufflinks 2.2.1: samtools-0.1 dep is build only<commit_after>class Cufflinks < Formula
  homepage "http://cufflinks.cbcb.umd.edu/"
  url "http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.tar.gz"
  sha256 "e8316b66177914f14b3a0c317e436d386a46c4c212ca1b2326f89f8a2e08d5ae"

  bottle do
    root_url "https://homebrew.bintray.com/bottles-science"
    cellar :any
    sha256 "68750a99e5cf104666cfc068c4bfddf8c2aebe2cb44bf5360aac2b5f4e181000" => :yosemite
    sha256 "3313084062765bee932d05d0bc8477887ec6a61e788c9a465c907cc363b44370" => :mavericks
    sha256 "d1e789b72fe73af8cb46aa71feeedea398df2c4b1e9fce5604492a7945143487" => :mountain_lion
  end

  depends_on "homebrew/versions/boost155" => :build
  depends_on "samtools-0.1" => :build
  depends_on "eigen"

  def install
    ENV["EIGEN_CPPFLAGS"] = "-I#{Formula["eigen"].opt_include}/eigen3"
    ENV.append "LIBS", "-lboost_system-mt -lboost_thread-mt -lboost_serialization-mt"
    system "./configure", "--disable-debug",
                          "--disable-dependency-tracking",
                          "--prefix=#{prefix}",
                          "--mandir=#{man}"
    system "make"
    ENV.j1
    system "make", "install"
  end
{'fraction_non_alphanumeric': 0.12301255230125523, 'fraction_numerical': 0.15690376569037656, 'mean_word_length': 3.5028248587570623, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 12, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2070809', 'n_tokens_mistral': 1159, 'n_tokens_neox': 977, 'n_words': 114}