class Igv < Formula
  desc "Interactive Genomics Viewer"
  homepage "https://www.broadinstitute.org/software/igv"
  url "https://data.broadinstitute.org/igv/projects/downloads/2.5/IGV_2.5.3.zip"
  sha256 "d33f6e20aaf5158770c6154953b8b3df89ced0f9416b399502864d3ccd44f22a"
  revision 1

  bottle :unneeded

  depends_on :java

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

  test do
    assert_match "Usage:", shell_output("#{bin}/igvtools")
    assert_match "org/broad/igv/ui/IGV.class", shell_output("jar tf #{libexec}/lib/igv.jar")
    # Fails on Jenkins with Unhandled exception: java.awt.HeadlessException
    unless ENV["CI"]
      (testpath/"script").write "exit"
      assert_match "Version", shell_output("#{bin}/igv -b script")
    end
  end
end