homebrew-core/Formula/snakemake.rb

class Snakemake < Formula
  include Language::Python::Virtualenv

  desc "Pythonic workflow system"
  homepage "https://snakemake.readthedocs.io/"
  url "https://files.pythonhosted.org/packages/b9/8b/61689a6501f908be53ec4fa58f47cda72061327863eac39b8000aeae6855/snakemake-5.19.3.tar.gz"
  sha256 "b83f3ef73e25dafcb39b3565030e33fa2f7e80ed70256c535dc7e58ea762305d"
  head "https://github.com/snakemake/snakemake.git"

  bottle do
    cellar :any_skip_relocation
    sha256 "4f28f4cc4ac60686bdf12944480c826739c9c0186dc538e863a2f3a89ce49ec7" => :catalina
    sha256 "076e3a9147c99202bc1d96f85b9ad0feb1758e898028fd6ea7d2eded841652ea" => :mojave
    sha256 "e8c76d4611240c653e62ffcefd85df218f23089b6a1451f01536a9d4ddf593be" => :high_sierra
  end

  depends_on "python@3.8"

  resource "appdirs" do
    url "https://files.pythonhosted.org/packages/d7/d8/05696357e0311f5b5c316d7b95f46c669dd9c15aaeecbb48c7d0aeb88c40/appdirs-1.4.4.tar.gz"
    sha256 "7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"
  end

  resource "attrs" do
    url "https://files.pythonhosted.org/packages/98/c3/2c227e66b5e896e15ccdae2e00bbc69aa46e9a8ce8869cc5fa96310bf612/attrs-19.3.0.tar.gz"
    sha256 "f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72"
  end

  resource "certifi" do
    url "https://files.pythonhosted.org/packages/b4/19/53433f37a31543364c8676f30b291d128cdf4cd5b31b755b7890f8e89ac8/certifi-2020.4.5.2.tar.gz"
    sha256 "5ad7e9a056d25ffa5082862e36f119f7f7cec6457fa07ee2f8c339814b80c9b1"
  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/bb/79/3045743bb26ca2e44a1d317c37395462bfed82dbbd38e69a3280b63696ce/ConfigArgParse-1.2.3.tar.gz"
    sha256 "edd17be986d5c1ba2e307150b8e5f5107aba125f3574dddd02c85d5cdcfd37dc"
  end

  resource "datrie" do
    url "https://files.pythonhosted.org/packages/9d/fe/db74bd405d515f06657f11ad529878fd389576dca4812bea6f98d9b31574/datrie-0.8.2.tar.gz"
    sha256 "525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d"
  end

  resource "decorator" do
    url "https://files.pythonhosted.org/packages/da/93/84fa12f2dc341f8cf5f022ee09e109961055749df2d0c75c5f98746cfe6c/decorator-4.4.2.tar.gz"
    sha256 "e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7"
  end

  resource "docutils" do
    url "https://files.pythonhosted.org/packages/2f/e0/3d435b34abd2d62e8206171892f174b180cd37b09d57b924ca5c2ef2219d/docutils-0.16.tar.gz"
    sha256 "c2de3a60e9e7d07be26b7f2b00ca0309c207e06c100f9cc2a94931fc75a478fc"
  end

  resource "gitdb" do
    url "https://files.pythonhosted.org/packages/d1/05/eaf2ac564344030d8b3ce870b116d7bb559020163e80d9aa4a3d75f3e820/gitdb-4.0.5.tar.gz"
    sha256 "c9e1f2d0db7ddb9a704c2a0217be31214e91a4fe1dea1efad19ae42ba0c285c9"
  end

  resource "GitPython" do
    url "https://files.pythonhosted.org/packages/5b/ef/96dd6b06400821bbad3f7e275f4a4f88af324124c5c04958e2f2c14ce2c8/GitPython-3.1.3.tar.gz"
    sha256 "e107af4d873daed64648b4f4beb89f89f0cfbe3ef558fc7821ed2331c2f8da1a"
  end

  resource "idna" do
    url "https://files.pythonhosted.org/packages/cb/19/57503b5de719ee45e83472f339f617b0c01ad75cba44aba1e4c97c2b0abd/idna-2.9.tar.gz"
    sha256 "7588d1c14ae4c77d74036e8c22ff447b26d0fde8f007354fd48a7814db15b7cb"
  end

  resource "ipython_genutils" do
    url "https://files.pythonhosted.org/packages/e8/69/fbeffffc05236398ebfcfb512b6d2511c622871dca1746361006da310399/ipython_genutils-0.2.0.tar.gz"
    sha256 "eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8"
  end

  resource "jsonschema" do
    url "https://files.pythonhosted.org/packages/69/11/a69e2a3c01b324a77d3a7c0570faa372e8448b666300c4117a516f8b1212/jsonschema-3.2.0.tar.gz"
    sha256 "c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a"
  end

  resource "jupyter-core" do
    url "https://files.pythonhosted.org/packages/28/64/8bdde111be57a2a3d54376db29b5f25ab9c68ffd3d6554989db24d5c1b7a/jupyter_core-4.6.3.tar.gz"
    sha256 "394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e"
  end

  resource "nbformat" do
    url "https://files.pythonhosted.org/packages/95/8e/8ffd07ed059a6277fe2f72d1fa411b49a8e512ad62f2ed20b9c2438192dd/nbformat-5.0.7.tar.gz"
    sha256 "54d4d6354835a936bad7e8182dcd003ca3dc0cedfee5a306090e04854343b340"
  end

  resource "psutil" do
    url "https://files.pythonhosted.org/packages/c4/b8/3512f0e93e0db23a71d82485ba256071ebef99b227351f0f5540f744af41/psutil-5.7.0.tar.gz"
    sha256 "685ec16ca14d079455892f25bd124df26ff9137664af445563c1bd36629b5e0e"
  end

  resource "pyrsistent" do
    url "https://files.pythonhosted.org/packages/9f/0d/cbca4d0bbc5671822a59f270e4ce3f2195f8a899c97d0d5abb81b191efb5/pyrsistent-0.16.0.tar.gz"
    sha256 "28669905fe725965daa16184933676547c5bb40a5153055a8dee2a4bd7933ad3"
  end

  resource "PyYAML" do
    url "https://files.pythonhosted.org/packages/64/c2/b80047c7ac2478f9501676c988a5411ed5572f35d1beff9cae07d321512c/PyYAML-5.3.1.tar.gz"
    sha256 "b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d"
  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/f5/4f/280162d4bd4d8aad241a21aecff7a6e46891b905a4341e7ab549ebaf7915/requests-2.23.0.tar.gz"
    sha256 "b3f43d496c6daba4493e7c431722aeb7dbc6288f52a6e04e7b6023b0247817e6"
  end

  resource "six" do
    url "https://files.pythonhosted.org/packages/6b/34/415834bfdafca3c5f451532e8a8d9ba89a21c9743a0c59fbd0205c7f9426/six-1.15.0.tar.gz"
    sha256 "30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259"
  end

  resource "smmap" do
    url "https://files.pythonhosted.org/packages/75/fb/2f594e5364f9c986b2c89eb662fc6067292cb3df2b88ae31c939b9138bb9/smmap-3.0.4.tar.gz"
    sha256 "9c98bbd1f9786d22f14b3d4126894d56befb835ec90cef151af566c7e19b5d24"
  end

  resource "toposort" do
    url "https://files.pythonhosted.org/packages/e5/d8/9bc1598ddf74410beba243ffeaee8d0b3ca7e9ac5cefe77367da497433e1/toposort-1.5.tar.gz"
    sha256 "dba5ae845296e3bf37b042c640870ffebcdeb8cd4df45adaa01d8c5476c557dd"
  end

  resource "traitlets" do
    url "https://files.pythonhosted.org/packages/75/b0/43deb021bc943f18f07cbe3dac1d681626a48997b7ffa1e7fb14ef922b21/traitlets-4.3.3.tar.gz"
    sha256 "d023ee369ddd2763310e4c3eae1ff649689440d4ae59d7485eb4cfbbe3e359f7"
  end

  resource "urllib3" do
    url "https://files.pythonhosted.org/packages/05/8c/40cd6949373e23081b3ea20d5594ae523e681b6f472e600fbc95ed046a36/urllib3-1.25.9.tar.gz"
    sha256 "3018294ebefce6572a474f0604c2021e33b3fd8006ecd11d62107a5d2a963527"
  end

  resource "wrapt" do
    url "https://files.pythonhosted.org/packages/82/f7/e43cefbe88c5fd371f4cf0cf5eb3feccd07515af9fd6cf7dbf1d1793a797/wrapt-1.12.1.tar.gz"
    sha256 "b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7"
  end

  def install
    virtualenv_install_with_resources
  end

  test do
    (testpath/"Snakefile").write <<~EOS
      rule testme:
          output:
               "test.out"
          shell:
               "touch {output}"
    EOS
    test_output = shell_output("#{bin}/snakemake --cores 1 -s #{testpath}/Snakefile 2>&1")
    assert_predicate testpath/"test.out", :exist?
    assert_match "Building DAG of jobs...", test_output
  end
end