homebrew-core/Formula/snakemake.rb

class Snakemake < Formula
  desc "Pythonic workflow system"
  homepage "https://snakemake.readthedocs.io/"
  url "https://files.pythonhosted.org/packages/a7/a0/ebafb2982558837824fd7a63ea73c68d07d81f99d1c1c0f3a05161da417c/snakemake-5.1.5.tar.gz"
  sha256 "9e5d8ab6cba6c1e7cb2c6f4118dc6052b07480c90c9a68781d8482d151ebec2f"
  revision 1
  head "https://bitbucket.org/snakemake/snakemake.git"

  bottle do
    cellar :any
    sha256 "875123fd82d9182dd228dcf590baf0759c6d9ecf4e0208bd256501d27f49322c" => :high_sierra
    sha256 "d71b5a0276cafda68a2b993ad0124f82ab957e94e625aa4de66d19077b49b2fa" => :sierra
    sha256 "808fce894185c5f0204932a4ce9c05ed3a2b37758a07557b6737bed92fdba9b5" => :el_capitan
  end

  depends_on "python"

  resource "Cython" do
    url "https://files.pythonhosted.org/packages/b3/ae/971d3b936a7ad10e65cb7672356cff156000c5132cf406cb0f4d7a980fd3/Cython-0.28.3.tar.gz"
    sha256 "1aae6d6e9858888144cea147eb5e677830f45faaff3d305d77378c3cba55f526"
  end

  resource "appdirs" do
    url "https://files.pythonhosted.org/packages/48/69/d87c60746b393309ca30761f8e2b49473d43450b150cb08f3c6df5c11be5/appdirs-1.4.3.tar.gz"
    sha256 "9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92"
  end

  resource "certifi" do
    url "https://files.pythonhosted.org/packages/4d/9c/46e950a6f4d6b4be571ddcae21e7bc846fcbb88f1de3eff0f6dd0a6be55d/certifi-2018.4.16.tar.gz"
    sha256 "13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7"
  end

  resource "chardet" do
    url "https://files.pythonhosted.org/packages/fc/bb/a5768c230f9ddb03acc9ef3f0d4a3cf93462473795d18e9535498c8f929d/chardet-3.0.4.tar.gz"
    sha256 "84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae"
  end

  resource "ConfigArgParse" do
    url "https://files.pythonhosted.org/packages/77/61/ae928ce6ab85d4479ea198488cf5ffa371bd4ece2030c0ee85ff668deac5/ConfigArgParse-0.13.0.tar.gz"
    sha256 "e6441aa58e23d3d122055808e5e2220fd742dff6e1e51082d2a4e4ed145dd788"
  end

  resource "datrie" do
    url "https://files.pythonhosted.org/packages/44/5f/bf7e4711f6aa95edb2216b3487eeac719645802259643d341668e65636db/datrie-0.7.1.tar.gz"
    sha256 "7a11371cc2dbbad71d6dfef57ced6e8b384bb377eeb847c63d58f8dc8e8b2023"
  end

  resource "decorator" do
    url "https://files.pythonhosted.org/packages/6f/24/15a229626c775aae5806312f6bf1e2a73785be3402c0acdec5dbddd8c11e/decorator-4.3.0.tar.gz"
    sha256 "c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c"
  end

  resource "docutils" do
    url "https://files.pythonhosted.org/packages/84/f4/5771e41fdf52aabebbadecc9381d11dea0fa34e4759b4071244fa094804c/docutils-0.14.tar.gz"
    sha256 "51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274"
  end

  resource "idna" do
    url "https://files.pythonhosted.org/packages/65/c4/80f97e9c9628f3cac9b98bfca0402ede54e0563b56482e3e6e45c43c4935/idna-2.7.tar.gz"
    sha256 "684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16"
  end

  resource "Jinja2" do
    url "https://files.pythonhosted.org/packages/56/e6/332789f295cf22308386cf5bbd1f4e00ed11484299c5d7383378cf48ba47/Jinja2-2.10.tar.gz"
    sha256 "f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4"
  end

  resource "jsonschema" do
    url "https://files.pythonhosted.org/packages/58/b9/171dbb07e18c6346090a37f03c7e74410a1a56123f847efed59af260a298/jsonschema-2.6.0.tar.gz"
    sha256 "6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02"
  end

  resource "MarkupSafe" do
    url "https://files.pythonhosted.org/packages/4d/de/32d741db316d8fdb7680822dd37001ef7a448255de9699ab4bfcbdf4172b/MarkupSafe-1.0.tar.gz"
    sha256 "a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665"
  end

  resource "networkx" do
    url "https://files.pythonhosted.org/packages/11/42/f951cc6838a4dff6ce57211c4d7f8444809ccbe2134179950301e5c4c83c/networkx-2.1.zip"
    sha256 "64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1"
  end

  resource "PyYAML" do
    url "https://files.pythonhosted.org/packages/bd/da/0a49c1a31c60634b93fd1376b3b7966c4f81f2da8263f389cad5b6bbd6e8/PyYAML-4.2b1.tar.gz"
    sha256 "ef3a0d5a5e950747f4a39ed7b204e036b37f9bddc7551c1a813b8727515a832e"
  end

  resource "ratelimiter" do
    url "https://files.pythonhosted.org/packages/5b/e0/b36010bddcf91444ff51179c076e4a09c513674a56758d7cfea4f6520e29/ratelimiter-1.2.0.post0.tar.gz"
    sha256 "5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7"
  end

  resource "requests" do
    url "https://files.pythonhosted.org/packages/54/1f/782a5734931ddf2e1494e4cd615a51ff98e1879cbe9eecbdfeaf09aa75e9/requests-2.19.1.tar.gz"
    sha256 "ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a"
  end

  resource "urllib3" do
    url "https://files.pythonhosted.org/packages/3c/d2/dc5471622bd200db1cd9319e02e71bc655e9ea27b8e0ce65fc69de0dac15/urllib3-1.23.tar.gz"
    sha256 "a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf"
  end

  resource "wrapt" do
    url "https://files.pythonhosted.org/packages/a0/47/66897906448185fcb77fc3c2b1bc20ed0ecca81a0f2f88eda3fc5a34fc3d/wrapt-1.10.11.tar.gz"
    sha256 "d4d560d479f2c21e1b5443bbd15fe7ec4b37fe7e53d335d3b9b0a7b1226fe3c6"
  end

  def install
    inreplace "snakemake/shell.py", "async", "async_" # Python 3.7 compat

    xy = Language::Python.major_minor_version "python3"

    ENV.prepend_create_path "PYTHONPATH", buildpath/"cython/lib/python#{xy}/site-packages"

    resource("Cython").stage do
      system "python3", *Language::Python.setup_install_args(buildpath/"cython")
    end

    ENV.prepend_path "PATH", buildpath/"cython/bin"

    resource("datrie").stage do
      system "./update_c.sh"
      ENV.delete "PYTHONPATH"
      ENV.prepend_create_path "PYTHONPATH", libexec/"vendor/lib/python#{xy}/site-packages"
      system "python3", *Language::Python.setup_install_args(libexec/"vendor")
    end

    resources.each do |r|
      next if r.name == "datrie" || r.name == "Cython"
      r.stage do
        system "python3", *Language::Python.setup_install_args(libexec/"vendor")
      end
    end

    ENV.prepend_create_path "PYTHONPATH", libexec/"lib/python#{xy}/site-packages"
    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
    (testpath/"Snakefile").write <<~EOS
      rule testme:
          output:
               "test.out"
          shell:
               "touch {output}"
    EOS
    system "#{bin}/snakemake"
  end
end