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Update docs with meta-recipe info
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‎GGD-CLI.html‎

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<meta charset="utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>GGD Commands &#8212; GGD documentation</title>
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<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
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<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
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<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
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<link rel="stylesheet" type="text/css" href="_static/style.css" />
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<link rel="stylesheet" type="text/css" href="_static/font-awesome-4.7.0/css/font-awesome.min.css" />
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<script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
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<script src="_static/jquery.js"></script>
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<script src="_static/underscore.js"></script>
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<script src="_static/doctools.js"></script>
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<script src="_static/language_data.js"></script>
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<link rel="index" title="Index" href="genindex.html" />
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<link rel="search" title="Search" href="search.html" />
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<link rel="next" title="ggd search" href="ggd-search.html" />
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<li class="toctree-l2"><a class="reference internal" href="pkg-info.html">ggd pkg-info</a></li>
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<li class="toctree-l2"><a class="reference internal" href="show-env.html">ggd show-env</a></li>
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<li class="toctree-l2"><a class="reference internal" href="make-recipe.html">ggd make-recipe</a></li>
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<li class="toctree-l2"><a class="reference internal" href="make-metarecipe.html">ggd make-meta-recipe</a></li>
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<li class="toctree-l2"><a class="reference internal" href="check-recipe.html">ggd check-recipe</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="meta-recipes.html">GGD meta-recipes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="contribute.html">Contribute</a></li>
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<li class="toctree-l1"><a class="reference internal" href="private_recipes.html">Private Recipes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="recipes.html">Available Data Packages</a></li>
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<p>Tabs for each tool are also available on the left tab bar.</p>
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<table class="docutils align-default">
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<colgroup>
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<col style="width: 42%" />
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<col style="width: 58%" />
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<col style="width: 43%" />
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<col style="width: 57%" />
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</colgroup>
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<thead>
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<tr class="row-odd"><th class="head"><p>Command</p></th>
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<tr class="row-even"><td><p><a class="reference internal" href="make-recipe.html#ggd-make-recipe"><span class="std std-ref">ggd make-recipe</span></a></p></td>
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<td><p>Create a ggd recipe from a bash script</p></td>
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</tr>
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<tr class="row-odd"><td><p><a class="reference internal" href="check-recipe.html#ggd-check-recipe"><span class="std std-ref">ggd check-recipe</span></a></p></td>
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<tr class="row-odd"><td><p><a class="reference internal" href="make-metarecipe.html#ggd-make-meta-recipe"><span class="std std-ref">ggd make-meta-recipe</span></a></p></td>
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<td><p>Create a ggd meta-recipe from a single or group of script</p></td>
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</tr>
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<tr class="row-even"><td><p><a class="reference internal" href="check-recipe.html#ggd-check-recipe"><span class="std std-ref">ggd check-recipe</span></a></p></td>
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<td><p>Check/test a ggd recipe</p></td>
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</tr>
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</tbody>
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<li class="toctree-l2"><a class="reference internal" href="make-recipe.html#examples">Examples</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="make-metarecipe.html">ggd make-meta-recipe</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="make-metarecipe.html#using-ggd-make-meta-recipe">Using ggd make-meta-recipe</a></li>
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<li class="toctree-l2"><a class="reference internal" href="make-metarecipe.html#examples">Examples</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="check-recipe.html">ggd check-recipe</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="check-recipe.html#check-recipe-is-used-to-validate-a-recipe-created-from-running-ggd-make-recipe"><cite>check-recipe</cite> is used to validate a recipe created from running <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">make-recipe</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="check-recipe.html#using-ggd-check-recipe">Using ggd check-recipe</a></li>

‎_sources/GGD-CLI.rst.txt‎

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Tabs for each tool are also available on the left tab bar.
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+-------------------------------------------------+--------------------------------------------------------------------+
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| Command | Description |
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+=================================================+====================================================================+
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| :ref:`ggd search <ggd-search>` | Search for a ggd data package |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd predict-path <ggd-predict-path>` | Predict the file path of a data package that has not been |
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| | installed yet (Good for workflows like Snakemake) |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd install <ggd-install>` | Install ggd data package(s) |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd uninstall <ggd-uninstall>` | Uninstall a ggd data package(s) |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd list <ggd-list>` | List the installed data packages (in a specific environment) |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd get-files <ggd-get-files>` | get the files for an installed ggd package |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd pkg-info <ggd-pkg-info>` | Show a specific ggd package's info |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd show-env <ggd-show-env>` | Show the ggd specific environment variables |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd make-recipe <ggd-make-recipe>` | Create a ggd recipe from a bash script |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd check-recipe <ggd-check-recipe>` | Check/test a ggd recipe |
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+-------------------------------------------------+--------------------------------------------------------------------+
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+----------------------------------------------------+--------------------------------------------------------------------+
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| Command | Description |
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+====================================================+====================================================================+
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| :ref:`ggd search <ggd-search>` | Search for a ggd data package |
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+----------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd predict-path <ggd-predict-path>` | Predict the file path of a data package that has not been |
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| | installed yet (Good for workflows like Snakemake) |
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+----------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd install <ggd-install>` | Install ggd data package(s) |
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+----------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd uninstall <ggd-uninstall>` | Uninstall a ggd data package(s) |
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+----------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd list <ggd-list>` | List the installed data packages (in a specific environment) |
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+----------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd get-files <ggd-get-files>` | get the files for an installed ggd package |
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+----------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd pkg-info <ggd-pkg-info>` | Show a specific ggd package's info |
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+----------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd show-env <ggd-show-env>` | Show the ggd specific environment variables |
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+----------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd make-recipe <ggd-make-recipe>` | Create a ggd recipe from a bash script |
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+----------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd make-meta-recipe <ggd-make-meta-recipe>` | Create a ggd meta-recipe from a single or group of script |
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+----------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd check-recipe <ggd-check-recipe>` | Check/test a ggd recipe |
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+----------------------------------------------------+--------------------------------------------------------------------+
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Command links:
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.. toctree::
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:maxdepth: 2
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ggd-search
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install
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predict-path
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uninstall
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list
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list-file
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pkg-info
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show-env
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make-recipe
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check-recipe
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:maxdepth: 2
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ggd-search
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install
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predict-path
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uninstall
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list
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list-file
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pkg-info
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show-env
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make-recipe
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make-metarecipe
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check-recipe

‎_sources/check-recipe.rst.txt‎

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| | local package installed) set this flag "-- |
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| | dont_uninstall" |
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+-----------------------+----------------------------------------------------------------------------------+
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| ``--id``, | If checking a meta-recipe the associated meta-recipe id needs to be supplied. |
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| ``(meta-recipe ID)`` | (Example: for a geo meta-recipe use something like --id GSE123) NOTE: GGD does |
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| | not try to correct the ID. Please provide the correct case sensitive ID. |
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+-----------------------+----------------------------------------------------------------------------------+
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| ``recipe_path`` | **Required** Path to recipe directory (can also be path to the .bz2) |
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+-----------------------+----------------------------------------------------------------------------------+
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The default functionality for `check-recipe` is to uninstall that file once the tests have finished. If you would like
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to keep the local data package installed add :code:`-du` to your `check-recipe` command.
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* *id:* The :code:`--id` parameter is used to designate the ID to use when checking a meta-recipe. This ID is required in order
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to check the meta-recipe. The ID represents a unique identifier that the meta-recipe can used to download data from the
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database the meta-recipe is created for. The ID entered is based on an ID that can be used by the specific meta-recipe being
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checked. NOTE: GGD does not try to fix IDs. They must be entered correctly including being
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case sensitive with proper alphanumeric order.
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The only required argument is the :code:`recipe_path` and refers to the directory you would like ``ggd check-recipe``
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to check. When using :ref:`ggd make-recipe <ggd-make-recipe>` to create a ggd recipe, make-recipe will
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create a new directory with four new files. The recipe_path should be the path to the new directory created
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from using `ggd make-recipe`.
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.. note::
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The :code:`--id` parameter is required if checking a meta-recipe
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Running :code:`ggd check-recipe <recipe-path>` will build, install, and test and validate the recipe to ensure the recipe works correctly.
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Example
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Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away.
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WARNING:conda_build.build:Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away.
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WARNING conda_build.build:bundle_conda(1030): Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away.
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INFO:conda_build.variants:Adding in variants from /scratch/local/u1138933/tmpn3m0b150/info/recipe/conda_build_config.yaml
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INFO conda_build.variants:_combine_spec_dictionaries(189): Adding in variants from /scratch/local/u1138933/tmpn3m0b150/info/recipe/conda_build_config.yaml
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INFO:conda_build.variants:Adding in variants from /scratch/tmpn3m0b150/info/recipe/conda_build_config.yaml
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INFO conda_build.variants:_combine_spec_dictionaries(189): Adding in variants from /scratch/local/tmpn3m0b150/info/recipe/conda_build_config.yaml
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Collecting package metadata (current_repodata.json): ...working... Unable to retrieve repodata (response: 404) for https://conda.anaconda.org/ggd-genomics/linux-64/current_repodata.json
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:ggd:uninstall: Removing hg19-phastcons-ucsc-v1 version 1 file(s) from ggd recipe storage
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:ggd:uninstall: Deleteing 10 items of hg19-phastcons-ucsc-v1 version 1 from your conda root
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:ggd:uninstall: Deleting 10 items of hg19-phastcons-ucsc-v1 version 1 from your conda root
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:ggd:env: Removing the ggd_hg19_phastcons_ucsc_v1_dir environment variable
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‎_sources/contribute-recipe.rst.txt‎

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[:ref:`Click here to return to the home page <home-page>`]
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This page is specific to creating a ggd **recipe**. For information on creating a meta-recipe see :ref:`Creating a ggd meta-recipe <contribute-meta-recipe>`
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The following steps outline how to create, check, and add a ggd data recipe.
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1. Update local forked repo

‎_sources/contribute.rst.txt‎

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* You will need a github account and a forked repository of ggd-recipes.
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* Once you have a github account and you have a forked ggd-recipes repo, you do not need to do step 1 again.
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2. :ref:`Make a ggd recipe <contrib-recipe>`
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2a. :ref:`Make a ggd recipe <contrib-recipe>`
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* The following steps will outline how to create a ggd data recipe, how to test it, and how to add it to the
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gogetdata/ggd-recipes repo.
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2b. :ref:`Make a ggd meta-recipe <contribute-meta-recipe>`
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* The following steps will outline how to create a ggd data meta-recipe, how to test it, and how to add it
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to the gogetdata/ggd-recipe repo.
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3. Continuous Integration testing with Circle CI
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* We use Circle CI to test all new recipes. Any recipe that passes will be officially added to the ggd repo
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github-setup
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contribute-recipe
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making-meta-recipes

‎_sources/index.rst.txt‎

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.. image:: Data_managment.png
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GGD meta-recipes
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----------------
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meta-recipes are recipes that provide access to a database of data using an identifier specific to that database. This is different then a normal ggd recipe,
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which consists of a set of instructions for a specific data file(s) to be installed and processed. Meta-recipes are powerful tools to provide access to database
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with large amounts of data which would be unreasonable to create a specific ggd recipe for individual data types/identifiers.
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For more information about meta-recipes see: :ref:`Meta-Recipes <meta-recipes>`
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========
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Example:
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quick-start
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using-ggd
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GGD-CLI
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meta-recipes
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contribute
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private_recipes
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recipes

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