<commit_before>class Salmon < Formula
  desc "Transcript-level quantification from RNA-seq reads"
  homepage "https://github.com/COMBINE-lab/salmon"
  # tag "bioinformatics"

  url "https://github.com/COMBINE-lab/salmon/archive/v0.7.0.tar.gz"
  sha256 "b0c30941814760095d6d302f7c3c74be0fc098c2851ff0fd58dd171ed1f8b4d8"

  head "https://github.com/COMBINE-lab/salmon.git"

  bottle do
    cellar :any
    sha256 "701fe4ff264c88522a12b90cceafc1de09149b2509934ea97adbf526bbcf2ba8" => :el_capitan
    sha256 "585ed6734572b41c62f51548a39a4064d4f69915f38a2851e7cac60425d42539" => :yosemite
  end

  # See https://github.com/kingsfordgroup/sailfish/issues/74
  needs :cxx11

  depends_on "autoconf" => :build
  depends_on "automake" => :build
  depends_on "cmake" => :build
  depends_on "boost"
  depends_on "tbb"
  depends_on "xz"
  depends_on "zlib" unless OS.mac?

  def install
    # Fix error: Unable to find the requested Boost libraries.
    ENV.deparallelize

    system "cmake", ".", *std_cmake_args
    system "make", "install"
  end

  test do
    system "#{bin}/salmon", "--version"
  end
end
<commit_msg>salmon: update 0.7.0 bottle for Linuxbrew.<commit_after>class Salmon < Formula
  desc "Transcript-level quantification from RNA-seq reads"
  homepage "https://github.com/COMBINE-lab/salmon"
  # tag "bioinformatics"

  url "https://github.com/COMBINE-lab/salmon/archive/v0.7.0.tar.gz"
  sha256 "b0c30941814760095d6d302f7c3c74be0fc098c2851ff0fd58dd171ed1f8b4d8"

  head "https://github.com/COMBINE-lab/salmon.git"

  bottle do
    cellar :any
    sha256 "701fe4ff264c88522a12b90cceafc1de09149b2509934ea97adbf526bbcf2ba8" => :el_capitan
    sha256 "585ed6734572b41c62f51548a39a4064d4f69915f38a2851e7cac60425d42539" => :yosemite
    sha256 "5a514675dc1d6e76d14535b9ff48feca8534addd9bbea83b95b36113585f24cc" => :x86_64_linux
  end

  # See https://github.com/kingsfordgroup/sailfish/issues/74
  needs :cxx11

  depends_on "autoconf" => :build
  depends_on "automake" => :build
  depends_on "cmake" => :build
  depends_on "boost"
  depends_on "tbb"
  depends_on "xz"
  depends_on "zlib" unless OS.mac?

  def install
    # Fix error: Unable to find the requested Boost libraries.
    ENV.deparallelize

    system "cmake", ".", *std_cmake_args
    system "make", "install"
  end

  test do
    system "#{bin}/salmon", "--version"
  end
end

{'fraction_non_alphanumeric': 0.10708191126279863, 'fraction_numerical': 0.1407849829351536, 'mean_word_length': 4.317460317460317, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 14, 'https://': 8, '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': '6215364', 'n_tokens_mistral': 1148, 'n_tokens_neox': 972, 'n_words': 166}