homebrew-core/Formula/snakemake.rb

class Snakemake < Formula
  desc "Pythonic workflow system"
  homepage "https://snakemake.readthedocs.io/"
  url "https://files.pythonhosted.org/packages/5a/a5/704ff1f58a121acf8b96f13a9b0abdbbb27a1a78cf52c676bd0bbd2c5f40/snakemake-5.2.2.tar.gz"
  sha256 "adffe7e24b4a613a9e8bf0a2a320b3cea236d86afb9132bb0bbbc08b8e35a3a3"
  head "https://bitbucket.org/snakemake/snakemake.git"

  bottle do
    cellar :any_skip_relocation
    sha256 "a534e048f08709c3dc1a0e4b4469acb2c180c8d26f8656901b0054bd5d4c371c" => :mojave
    sha256 "eb9e3e7ff32688eea43f615c0938d24d6ca403f9af7f87721f80621fdee5a693" => :high_sierra
    sha256 "ca80f328a2539740627e14ebdd6cc47c42ab2f62bb651a966e77fdbcd1ee5eff" => :sierra
    sha256 "208698739662d1f1a8285ddec094f4779be4a12dba4808f664b23ac2e50e5511" => :el_capitan
  end

  depends_on "python"

  resource "Cython" do
    url "https://files.pythonhosted.org/packages/d2/12/8ef44cede251b93322e8503fd6e1b25a0249fa498bebec191a5a06adbe51/Cython-0.28.4.tar.gz"
    sha256 "76ac2b08d3d956d77b574bb43cbf1d37bd58b9d50c04ba281303e695854ebc46"
  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 "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 "jsonschema" do
    url "https://files.pythonhosted.org/packages/58/b9/171dbb07e18c6346090a37f03c7e74410a1a56123f847efed59af260a298/jsonschema-2.6.0.tar.gz"
    sha256 "6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02"
  end

  resource "PyYAML" do
    url "https://files.pythonhosted.org/packages/9e/a3/1d13970c3f36777c583f136c136f804d70f500168edc1edea6daa7200769/PyYAML-3.13.tar.gz"
    sha256 "3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf"
  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
    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