<commit_before>class Glimmerhmm < Formula
  homepage "https://ccb.jhu.edu/software/glimmerhmm/"
  # doi "10.1093/bioinformatics/bth315"
  # tag "bioinformatics"

  url "ftp://ccb.jhu.edu/pub/software/glimmerhmm/GlimmerHMM-3.0.4.tar.gz"
  sha256 "43e321792b9f49a3d78154cbe8ddd1fb747774dccb9e5c62fbcc37c6d0650727"

  bottle do
    cellar :any_skip_relocation
    sha256 "6c129f46df339601105a9bea74cc34ebd44bfefd70af9602db8728d6efca187b" => :high_sierra
    sha256 "bec2c26c9b1b965de11c91126e799151b14c41854deea4bd3f02e80e1170ceab" => :sierra
    sha256 "085de0bdee7ea9d218357d4d82fc2eed1963e1c3a7b1930b7f8da48f734d707a" => :el_capitan
  end

  def install
    # fatal error: 'malloc.h' file not found
    inreplace %w[sources/oc1.h sources/util.c train/utils.c], "malloc.h", "stdlib.h"

    system *%w[make -C sources]
    system *%w[make -C train]
    bin.install %w[sources/glimmerhmm bin/glimmhmm.pl]
    prefix.install Dir["*"] - %w[bin sources]
  end

  test do
    system "#{bin}/glimmerhmm", "-h"
  end
end
<commit_msg>glimmerhmm: update 3.0.4 bottle for Linuxbrew.<commit_after>class Glimmerhmm < Formula
  homepage "https://ccb.jhu.edu/software/glimmerhmm/"
  # doi "10.1093/bioinformatics/bth315"
  # tag "bioinformatics"

  url "ftp://ccb.jhu.edu/pub/software/glimmerhmm/GlimmerHMM-3.0.4.tar.gz"
  sha256 "43e321792b9f49a3d78154cbe8ddd1fb747774dccb9e5c62fbcc37c6d0650727"

  bottle do
    cellar :any_skip_relocation
    sha256 "6c129f46df339601105a9bea74cc34ebd44bfefd70af9602db8728d6efca187b" => :high_sierra
    sha256 "bec2c26c9b1b965de11c91126e799151b14c41854deea4bd3f02e80e1170ceab" => :sierra
    sha256 "085de0bdee7ea9d218357d4d82fc2eed1963e1c3a7b1930b7f8da48f734d707a" => :el_capitan
    sha256 "64ad84363d8dbe8c904d886748a84efabc536b3fab72516fb3c18977aba3d559" => :x86_64_linux
  end

  def install
    # fatal error: 'malloc.h' file not found
    inreplace %w[sources/oc1.h sources/util.c train/utils.c], "malloc.h", "stdlib.h"

    system *%w[make -C sources]
    system *%w[make -C train]
    bin.install %w[sources/glimmerhmm bin/glimmhmm.pl]
    prefix.install Dir["*"] - %w[bin sources]
  end

  test do
    system "#{bin}/glimmerhmm", "-h"
  end
end

{'fraction_non_alphanumeric': 0.11075367647058823, 'fraction_numerical': 0.18336397058823528, 'mean_word_length': 4.625322997416021, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 10, 'https://': 2, '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': '2826304', 'n_tokens_mistral': 1198, 'n_tokens_neox': 981, 'n_words': 136}