<commit_before>class Augustus < Formula
  desc "Predict genes in eukaryotic genomic sequences"
  homepage "http://bioinf.uni-greifswald.de/augustus/"
  url "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.tar.gz"
  sha256 "b5eb811a4c33a2cc3bbd16355e19d530eeac6d1ac923e59f48d7a79f396234ee"
  revision OS.mac? ? 1 : 2

  bottle do
    sha256 "6ffeac4edd4805321ea0957959f85da8cc1f5978cdc8a98903a78c407d5d183e" => :high_sierra
    sha256 "b87f6e5824186aaa1a02cc6665dde1328a4255aed653de85edd3e4bd40f65c60" => :sierra
    sha256 "19a761ef4afa0cd5e9699b59b11eaac2e7e1d3dbfa14e2c8ced1b27eb57c2c1e" => :el_capitan
  end

  depends_on "bamtools"
  depends_on "boost"
  unless OS.mac?
    depends_on "bamtools"
    depends_on "zlib"
  end

  def install
    # Fix error: api/BamReader.h: No such file or directory
    inreplace "auxprogs/bam2hints/Makefile",
      "INCLUDES = /usr/include/bamtools",
      "INCLUDES = #{Formula["bamtools"].include/"bamtools"}"
    inreplace "auxprogs/filterBam/src/Makefile",
      "BAMTOOLS = /usr/include/bamtools",
      "BAMTOOLS= #{Formula["bamtools"].include/"bamtools"}"

    # Prevent symlinking into /usr/local/bin/
    inreplace "Makefile", %r{ln -sf.*/usr/local/bin/}, "#ln -sf"

    # Compile executables for macOS. Tarball ships with executables for Linux.
    system "make", "clean"
    system "make"<commit_msg>augustus: update 3.3_2 bottle for Linuxbrew.<commit_after>class Augustus < Formula
  desc "Predict genes in eukaryotic genomic sequences"
  homepage "http://bioinf.uni-greifswald.de/augustus/"
  url "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.tar.gz"
  sha256 "b5eb811a4c33a2cc3bbd16355e19d530eeac6d1ac923e59f48d7a79f396234ee"
  revision OS.mac? ? 1 : 2

  bottle do
    sha256 "6ffeac4edd4805321ea0957959f85da8cc1f5978cdc8a98903a78c407d5d183e" => :high_sierra
    sha256 "b87f6e5824186aaa1a02cc6665dde1328a4255aed653de85edd3e4bd40f65c60" => :sierra
    sha256 "19a761ef4afa0cd5e9699b59b11eaac2e7e1d3dbfa14e2c8ced1b27eb57c2c1e" => :el_capitan
    sha256 "30cd29d89268db39060cd33e0cc87f108884b09d4fd5921dd451fc3f38ba3823" => :x86_64_linux
  end

  depends_on "bamtools"
  depends_on "boost"
  unless OS.mac?
    depends_on "bamtools"
    depends_on "zlib"
  end

  def install
    # Fix error: api/BamReader.h: No such file or directory
    inreplace "auxprogs/bam2hints/Makefile",
      "INCLUDES = /usr/include/bamtools",
      "INCLUDES = #{Formula["bamtools"].include/"bamtools"}"
    inreplace "auxprogs/filterBam/src/Makefile",
      "BAMTOOLS = /usr/include/bamtools",
      "BAMTOOLS= #{Formula["bamtools"].include/"bamtools"}"

    # Prevent symlinking into /usr/local/bin/
    inreplace "Makefile", %r{ln -sf.*/usr/local/bin/}, "#ln -sf"

    # Compile executables for macOS. Tarball ships with executables for Linux.
    system "make", "clean"
    system "make"
{'fraction_non_alphanumeric': 0.10994397759103641, 'fraction_numerical': 0.13165266106442577, 'mean_word_length': 4.390566037735849, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 10, 'https://': 0, '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': '6495587', 'n_tokens_mistral': 1399, 'n_tokens_neox': 1204, 'n_words': 187}