<commit_before>class Igv < Formula
  desc "Interactive Genomics Viewer"
  homepage "https://www.broadinstitute.org/software/igv"
  url "https://data.broadinstitute.org/igv/projects/downloads/2.15/IGV_2.15.1.zip"
  sha256 "2573ccbe559d4c26bcc3a93ff73a7befbb0176b5b31aa8aa189c0f076028be61"
  license "MIT"

  livecheck do
    url "https://software.broadinstitute.org/software/igv/download"
    regex(/href=.*?IGV[._-]v?(\d+(?:\.\d+)+)\.zip/i)
  end

  bottle do
    sha256 cellar: :any_skip_relocation, all: "b3eadc87f195d8921f2b10eaee33606099fb26eb07197ef537ed4c5945933f1c"
  end

  depends_on "openjdk"

  def install
    inreplace ["igv.sh", "igvtools"], /^prefix=.*/, "prefix=#{libexec}"
    bin.install "igv.sh" => "igv"
    bin.install "igvtools"
    libexec.install "igv.args", "lib"
    bin.env_script_all_files libexec, Language::Java.overridable_java_home_env
  end

  test do
    assert_match "Usage:", shell_output("#{bin}/igvtools")
    assert_match "org/broad/igv/ui/IGV.class", shell_output("#{Formula["openjdk"].bin}/jar tf #{libexec}/lib/igv.jar")

    ENV.append "_JAVA_OPTIONS", "-Duser.home=#{testpath}"
    (testpath/"script").write "exit"
    assert_match "Using system JDK.", shell_output("#{bin}/igv -b script")
  end
end
<commit_msg>igv: update 2.15.1 bottle.<commit_after>class Igv < Formula
  desc "Interactive Genomics Viewer"
  homepage "https://www.broadinstitute.org/software/igv"
  url "https://data.broadinstitute.org/igv/projects/downloads/2.15/IGV_2.15.1.zip"
  sha256 "2573ccbe559d4c26bcc3a93ff73a7befbb0176b5b31aa8aa189c0f076028be61"
  license "MIT"

  livecheck do
    url "https://software.broadinstitute.org/software/igv/download"
    regex(/href=.*?IGV[._-]v?(\d+(?:\.\d+)+)\.zip/i)
  end

  bottle do
    sha256 cellar: :any_skip_relocation, all: "7eaab68f53de0fbe0c806f437ecf4a1b02856f8aa24bd85995edf2fb5d5dd657"
  end

  depends_on "openjdk"

  def install
    inreplace ["igv.sh", "igvtools"], /^prefix=.*/, "prefix=#{libexec}"
    bin.install "igv.sh" => "igv"
    bin.install "igvtools"
    libexec.install "igv.args", "lib"
    bin.env_script_all_files libexec, Language::Java.overridable_java_home_env
  end

  test do
    assert_match "Usage:", shell_output("#{bin}/igvtools")
    assert_match "org/broad/igv/ui/IGV.class", shell_output("#{Formula["openjdk"].bin}/jar tf #{libexec}/lib/igv.jar")

    ENV.append "_JAVA_OPTIONS", "-Duser.home=#{testpath}"
    (testpath/"script").write "exit"
    assert_match "Using system JDK.", shell_output("#{bin}/igv -b script")
  end
end

{'fraction_non_alphanumeric': 0.15841584158415842, 'fraction_numerical': 0.06970297029702971, 'mean_word_length': 4.432258064516129, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 6, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1622746', 'n_tokens_mistral': 1126, 'n_tokens_neox': 1018, 'n_words': 151}