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‎GGD-CLI.html‎

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<head>
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<meta charset="utf-8" />
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<title>GGD Commands &#8212; GGD documentation</title>
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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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<link rel="prev" title="Using GGD" href="using-ggd.html" />
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</head><body>
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<div class="document">
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<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
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</a>
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</p>
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<h3>Navigation</h3>
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<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="quick-start.html">GGD Quick Start</a></li>
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<li class="toctree-l1"><a class="reference internal" href="using-ggd.html">Using GGD</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">GGD Commands</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="ggd-search.html">ggd search</a></li>
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<li class="toctree-l2"><a class="reference internal" href="install.html">ggd install</a></li>
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<li class="toctree-l2"><a class="reference internal" href="predict-path.html">ggd predict-path</a></li>
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<li class="toctree-l2"><a class="reference internal" href="uninstall.html">ggd uninstall</a></li>
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<li class="toctree-l2"><a class="reference internal" href="list.html">ggd list</a></li>
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<li class="toctree-l2"><a class="reference internal" href="list-file.html">ggd get-files</a></li>
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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="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="contribute.html">Contribute</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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</ul>
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<ul>
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<li class="toctree-l1"><a href="https://github.com/gogetdata/ggd-recipes">ggd-recipes @ Github</a></li>
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<li class="toctree-l1"><a href="https://github.com/gogetdata/ggd-cli">ggd-cli @ Github</a></li>
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</ul>
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<div id="searchbox" style="display: none" role="search">
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<h3 id="searchlabel">Quick search</h3>
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<form class="search" action="search.html" method="get">
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<input type="text" name="q" aria-labelledby="searchlabel" />
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</form>
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</div>
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</div>
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<script>$('#searchbox').show(0);</script>
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</div>
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</div>
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<div class="documentwrapper">
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<div class="bodywrapper">
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<div class="body" role="main">
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<div class="section" id="ggd-commands">
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<span id="ggd-cli-page"></span><h1>GGD Commands<a class="headerlink" href="#ggd-commands" title="Permalink to this headline"></a></h1>
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<p>[<a class="reference internal" href="index.html#home-page"><span class="std std-ref">Click here to return to the home page</span></a>]</p>
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<p>The ggd command line interface (cli) has multiple tools for data access and local management. Below you can find a short
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description of each tool, as well as links to specific pages about each.</p>
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<p>Tabs for each tool are also available on the left tab bar.</p>
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<ol class="arabic">
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<li><p><a class="reference internal" href="ggd-search.html#ggd-search"><span class="std std-ref">ggd search</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>Search for a ggd data package</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="predict-path.html#ggd-predict-path"><span class="std std-ref">ggd predict-path</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>Predict the file path of a data package that has not been installed yet (Good for workflows like Snakemake)</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="install.html#ggd-install"><span class="std std-ref">ggd install</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>Install ggd data package(s)</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="uninstall.html#ggd-uninstall"><span class="std std-ref">ggd uninstall</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>Uninstall a ggd data package(s)</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="list.html#ggd-list"><span class="std std-ref">ggd list</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>List the installed data packages (in a specific environment)</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="list-file.html#ggd-get-files"><span class="std std-ref">ggd get-files</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>get the files for an installed ggd package</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="pkg-info.html#ggd-pkg-info"><span class="std std-ref">ggd pkg-info</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>Show a specific ggd package’s info</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="show-env.html#ggd-show-env"><span class="std std-ref">ggd show-env</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>Show the ggd specific environment variables</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="make-recipe.html#ggd-make-recipe"><span class="std std-ref">ggd make-recipe</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>Create a ggd recipe from a bash script</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="check-recipe.html#ggd-check-recipe"><span class="std std-ref">ggd check-recipe</span></a></p>
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<ul class="simple">
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<li><p>Check/test a ggd recipe</p></li>
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</ul>
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</li>
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</ol>
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<p>Command links:</p>
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<div class="toctree-wrapper compound">
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="ggd-search.html">ggd search</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="ggd-search.html#using-ggd-search">Using ggd search</a></li>
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<li class="toctree-l2"><a class="reference internal" href="ggd-search.html#example">Example</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="install.html">ggd install</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="install.html#using-ggd-install">Using ggd install</a></li>
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<li class="toctree-l2"><a class="reference internal" href="install.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="predict-path.html">ggd predict-path</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="predict-path.html#using-ggd-predict-path">Using ggd predict-path</a></li>
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<li class="toctree-l2"><a class="reference internal" href="predict-path.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="uninstall.html">ggd uninstall</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="uninstall.html#using-ggd-uninstall">Using ggd uninstall</a></li>
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<li class="toctree-l2"><a class="reference internal" href="uninstall.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="list.html">ggd list</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="list.html#using-ggd-list">Using ggd list</a></li>
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<li class="toctree-l2"><a class="reference internal" href="list.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="list-file.html">ggd get-files</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="list-file.html#using-ggd-list-files">Using ggd list-files</a></li>
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<li class="toctree-l2"><a class="reference internal" href="list-file.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="pkg-info.html">ggd pkg-info</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="pkg-info.html#using-ggd-pkg-info">Using ggd pkg-info</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pkg-info.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="show-env.html">ggd show-env</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="show-env.html#using-ggd-show-env">Using ggd show-env</a></li>
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<li class="toctree-l2"><a class="reference internal" href="show-env.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-recipe.html">ggd make-recipe</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="make-recipe.html#using-ggd-make-recipe">Using ggd make-recipe</a></li>
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<li class="toctree-l2"><a class="reference internal" href="make-recipe.html#data-recipe-standards">Data recipe standards</a></li>
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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="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>
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<li class="toctree-l2"><a class="reference internal" href="check-recipe.html#example">Example</a></li>
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</ul>
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</li>
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</ul>
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</div>
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&copy;2016-2020, The GoGetData team.
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<a href="_sources/GGD-CLI.rst.txt"
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‎_sources/GGD-CLI.rst.txt‎

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.. _ggd_cli_page:
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GGD Commands
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============
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[:ref:`Click here to return to the home page <home-page>`]
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The ggd command line interface (cli) has multiple tools for data access and local management. Below you can find a short
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description of each tool, as well as links to specific pages about each.
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Tabs for each tool are also available on the left tab bar.
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1. :ref:`ggd search <ggd-search>`
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* Search for a ggd data package
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2. :ref:`ggd predict-path <ggd-predict-path>`
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* Predict the file path of a data package that has not been installed yet (Good for workflows like Snakemake)
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3. :ref:`ggd install <ggd-install>`
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* Install ggd data package(s)
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4. :ref:`ggd uninstall <ggd-uninstall>`
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* Uninstall a ggd data package(s)
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5. :ref:`ggd list <ggd-list>`
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* List the installed data packages (in a specific environment)
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6. :ref:`ggd get-files <ggd-get-files>`
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* get the files for an installed ggd package
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7. :ref:`ggd pkg-info <ggd-pkg-info>`
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* Show a specific ggd package's info
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8. :ref:`ggd show-env <ggd-show-env>`
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* Show the ggd specific environment variables
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9. :ref:`ggd make-recipe <ggd-make-recipe>`
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* Create a ggd recipe from a bash script
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10. :ref:`ggd check-recipe <ggd-check-recipe>`
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* Check/test a ggd recipe
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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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