<commit_before>class Tophat < Formula
  desc "Spliced read mapper for RNA-Seq"
  homepage "http://ccb.jhu.edu/software/tophat"
  url "http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz"
  sha256 "37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5"
  # doi "10.1093/bioinformatics/btp120"
  # tag "bioinformatics"
  revision 1

  bottle do
    cellar :any
    sha256 "186e8686503284e7ac3e0187388e5babaf1d5f07df07d6dbc27d91091becc505" => :el_capitan
    sha256 "f43d751a37fbe897315e450219392161becf97f445729d0dc007b8048687c3c7" => :yosemite
    sha256 "4f78eba798dbf5d23f237e87abdd5486b2fc874f6771fb0e1f8b6b1030cf37c1" => :mavericks
    sha256 "dedd0fa5a2cf7b3bd87431c9a3851c8f54231966a67406528501b804ff9ad5c0" => :x86_64_linux
  end

  depends_on "boost"
  depends_on "bowtie2"
  depends_on "bowtie" => :optional

  patch :p0, :DATA

  resource "test" do
    url "http://ccb.jhu.edu/software/tophat/downloads/test_data.tar.gz"
    sha256 "18840bd020dd23f4fe298d935c82f4b8ef7974de62ff755c21d7f88dc40054e1"
  end

  def install
    ENV.deparallelize
    ENV.append "LIBS", "-lboost_system-mt -lboost_thread-mt"

    resource("test").stage { (share/"test_data").install Dir["*"] }

    system "./configure", "--disable-dependency-tracking",
                          "--prefix=#{prefix}"
    system "make", "install"
<commit_msg>tophat: update 2.1.1_1 bottle.<commit_after>class Tophat < Formula
  desc "Spliced read mapper for RNA-Seq"
  homepage "http://ccb.jhu.edu/software/tophat"
  url "http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz"
  sha256 "37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5"
  # doi "10.1093/bioinformatics/btp120"
  # tag "bioinformatics"
  revision 1

  bottle do
    cellar :any
    sha256 "7c8cd03f1b5429a9458f23c3e89c1ca70a3bb66f86ea99830da78f6ca7df3060" => :el_capitan
    sha256 "9018f5952a79235bd3955522ac46ab0e94cbd489ec802f9295c24bd85ab204dd" => :yosemite
    sha256 "acd66232b41070f1fd1d5901a63f7306cbdb7793a7036c67b31a887c5be019dd" => :mavericks
  end

  depends_on "boost"
  depends_on "bowtie2"
  depends_on "bowtie" => :optional

  patch :p0, :DATA

  resource "test" do
    url "http://ccb.jhu.edu/software/tophat/downloads/test_data.tar.gz"
    sha256 "18840bd020dd23f4fe298d935c82f4b8ef7974de62ff755c21d7f88dc40054e1"
  end

  def install
    ENV.deparallelize
    ENV.append "LIBS", "-lboost_system-mt -lboost_thread-mt"

    resource("test").stage { (share/"test_data").install Dir["*"] }

    system "./configure", "--disable-dependency-tracking",
                          "--prefix=#{prefix}"
    system "make", "install"

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