circlator.rb

class Circlator < Formula
  desc "A tool to circularize genome assemblies"
  homepage "https://github.com/sanger-pathogens/circlator"
  url "https://github.com/sanger-pathogens/circlator/archive/v0.14.2.tar.gz"
  sha256 "fa8a6568a731ef5a996ffa024d03cfd85dfcddf624a5109e47a0bf2059bd0a9d"
  head "https://github.com/sanger-pathogens/circlator.git"
  revision 1

  bottle do
    cellar :any_skip_relocation
    sha256 "f4fb0d48fab19da0526fd85376b0d0d310d13d750bd090ad3b28bd1a4b9aecd3" => :yosemite
    sha256 "f28e1432d6b79e02da20cb1c4cc146c55b77155bb885b1f195ab9dc29fe9f674" => :mavericks
    sha256 "c24a31e8b4ac5488fc02bda87107a3761bce4e249f0309a5aef01f0d94aa0e39" => :mountain_lion
  end

  # tag "bioinformatics"

  depends_on "zlib" unless OS.mac?
  depends_on :python3
  depends_on "bwa"
  depends_on "prodigal"
  depends_on "samtools"
  depends_on "spades"
  depends_on "homebrew/python/numpy" => ["with-python3"]
  depends_on "homebrew/python/pymummer"

  resource "pysam" do
    url "https://pypi.python.org/packages/source/p/pysam/pysam-0.8.3.tar.gz"
    sha256 "343e91a1882278455ef9a5f3c9fc4921c37964341785bf22432381d18e6d115e"
  end

  resource "pyfastaq" do
    url "https://pypi.python.org/packages/source/p/pyfastaq/pyfastaq-3.5.0.tar.gz"
    sha256 "599b28db5a05072335eacd3cea458aff511239e34a9559aaf2e7fe94cce785a9"
  end

  resource "bio_assembly_refinement" do
    url "https://pypi.python.org/packages/source/b/bio_assembly_refinement/bio_assembly_refinement-0.3.2.tar.gz"
    sha256 "3b9dfe97afff1dcc8294ec8a6dc7aed1af77ea697dc1545247907678e800c610"
  end

  def install
    version = Language::Python.major_minor_version "python3"
    ENV.prepend_create_path "PYTHONPATH", libexec/"lib/python#{version}/site-packages"
    ENV.prepend_create_path "PYTHONPATH", libexec/"vendor/lib/python#{version}/site-packages"

    %w[pysam pyfastaq bio_assembly_refinement].each do |r|
      resource(r).stage do
        system "python3", *Language::Python.setup_install_args(libexec/"vendor")
      end
    end

    system "python3", *Language::Python.setup_install_args(libexec)
    bin.install Dir[libexec/"bin/*"]
    bin.env_script_all_files(libexec/"bin", :PYTHONPATH => ENV["PYTHONPATH"])
  end

  test do
    assert_match "Available commands", shell_output("circlator -h 2>&1", 0)
  end
end