poretools installation using homebrew

poretools.rb

class Poretools < Formula
  desc "Tools for working with nanopore sequencing data"
  homepage "http://poretools.readthedocs.org/"
  url "https://github.com/arq5x/poretools/archive/v0.5.1.tar.gz"
  sha256 "7cd55a8f30290992dcf8d7792401e7f21efadfde02b3f4604d6680d2f8300479"
  head "https://github.com/arq5x/poretools.git"

  depends_on "hdf5"
  depends_on "r"
  depends_on :python if MacOS.version <= :snow_leopard
  depends_on "openssl"

  resource "rpy2" do
    url "https://pypi.python.org/packages/source/r/rpy2/rpy2-2.5.6.tar.gz"
    sha256 "d0d584c435b5ed376925a95a4525dbe87de7fa9260117e9f208029e0c919ad06"
  end

  resource "Cython" do
    url "http://cython.org/release/Cython-0.22.tar.gz"
    sha256 "14307e7a69af9a0d0e0024d446af7e51cc0e3e4d0dfb10d36ba837e5e5844015"
  end

  resource "h5py" do
    url "https://pypi.python.org/packages/source/h/h5py/h5py-2.5.0.tar.gz#md5=6e4301b5ad5da0d51b0a1e5ac19e3b74"
    sha256 "9833df8a679e108b561670b245bcf9f3a827b10ccb3a5fa1341523852cfac2f6"
  end

  resource "six" do
    url "https://pypi.python.org/packages/source/s/six/six-1.9.0.tar.gz#md5=476881ef4012262dfc8adc645ee786c4"
    sha256 "e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5"
  end

  resource "watchdog" do
    url "https://pypi.python.org/packages/source/w/watchdog/watchdog-0.8.3.tar.gz"
    sha256 "7e65882adb7746039b6f3876ee174952f8eaaa34491ba34333ddf1fe35de4162"
  end

  resource "pathtools" do
    url "https://pypi.python.org/packages/source/p/pathtools/pathtools-0.1.2.tar.gz"
    sha256 "7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0"
  end

  resource "argh" do
    url "https://pypi.python.org/packages/source/a/argh/argh-0.26.1.tar.gz"
    sha256 "06a7442cb9130fb8806fe336000fcf20edf1f2f8ad205e7b62cec118505510db"
  end

  resource "PyYAML" do
    url "https://pypi.python.org/packages/source/P/PyYAML/PyYAML-3.11.tar.gz#md5=f50e08ef0fe55178479d3a618efe21db"
    sha256 "c36c938a872e5ff494938b33b14aaa156cb439ec67548fcab3535bb78b0846e8"
  end

  resource "singledispatch" do
    url "https://pypi.python.org/packages/source/s/singledispatch/singledispatch-3.4.0.3.tar.gz#md5=af2fc6a3d6cc5a02d0bf54d909785fcb"
    sha256 "5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c"
  end

  resource "codetools" do
    url "http://cran.r-project.org/src/contrib/codetools_0.2-11.tar.gz"
    sha256 "b02e8b17ea9173b73c20e84fbd36c420d5a79bb56a6b9d0d45c22a7d540f54d5"
  end

  resource "MASS" do
    url "http://cran.r-project.org/src/contrib/MASS_7.3-40.tar.gz"
    sha256 "9e0c937162cb485511ce77c8519a21558370c20f3c6dc34493b895cb355cb516"
  end

  resource "ggplot2" do
    url "http://cran.r-project.org/src/contrib/ggplot2_1.0.1.tar.gz"
    sha256 "40248e6b31307787e44e45d806e7a33095844a9bbe864cc7583dd311b19c241d"
  end

  resource "test" do
    url "ftp://ftp.sra.ebi.ac.uk/vol1/ERA412/ERA412821/oxfordnanopore_native/MVA_filtered.tar.gz"
    sha256 "76b00286acba1f65c76a3869bc60e099190ce48d0a5822606ce222e80529e523"
  end

  def install
    ENV.prepend_create_path "PYTHONPATH", libexec/"vendor/lib/python2.7/site-packages"
    ENV.prepend_create_path "R_LIBS", libexec/"vendor/R/library"
    ENV.prepend_create_path "PATH", libexec/"vendor/bin"

    respy = %w[rpy2 Cython h5py six watchdog pathtools argh PyYAML singledispatch]
    resr = %w[codetools MASS ggplot2]

    # install python dependencies
    respy.each do |rp|
      resource(rp).stage do
        system "python", *Language::Python.setup_install_args(libexec/"vendor")
      end
    end

    # install devtools
    system "R", "-q", "-e", "install.packages('devtools', lib='" + libexec/"vendor/R/library" + "', repos='http://cran.r-project.org')"

    # install r dependencies
    ENV.prepend "LDFLAGS", "-L" + Formula["openssl"].lib
    ENV.prepend "CPPFLAGS", "-I" + Formula["openssl"].include
    resr.each do |rr|
      resource(rr).stage do
        system "R", "-q", "-e", "library(devtools); install(pkg='.', lib='" + libexec/"vendor/R/library" + "')"
      end
    end

    # install poretools
    ENV.prepend_create_path "PYTHONPATH", libexec+"lib/python2.7/site-packages"
    system "python", *Language::Python.setup_install_args(libexec)

    libexec.install Dir[libexec/"bin/*"]
    libexec.env_script_all_files(libexec+"bin", :PYTHONPATH => ENV["PYTHONPATH"])
    (bin/"poretools").write_env_script(libexec+"bin/poretools", :R_LIBS => ENV["R_LIBS"], :PYTHONPATH => ENV["PYTHONPATH"])

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

  test do
    result = <<-EOS.undent
    total reads	297
    total base pairs	260131
    mean	875.86
    median	795
    min	325
    max	3602
    N25	965
    N50	830
    N75	741
    EOS

    assert_equal result, shell_output("#{bin}/poretools stats #{share}/test_data/")
  end
end

Would it be best to hard code all the resources in here and do an R CMD INSTALL . on them all, or can you provide a resource without a url and then I just iterate over with R -q -e install.packages()? Likewise, can I do that via pip install with the python dependencies? Installing within the poretools homebrew directory seems like it may create dependency issues when things need upgrading?

What tests would be relevant? Can I pull in data using the formula to test poretools functionality?

Submitted a pull request here https://github.com/Homebrew/homebrew-science/pull/2300.