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GGD-CLI.html
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<!DOCTYPE html>
<html>
<head>
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<title>GGD Commands — GGD documentation</title>
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<h3>Navigation</h3>
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<li class="toctree-l1"><a class="reference internal" href="quick-start.html">GGD Quick Start</a></li>
<li class="toctree-l1"><a class="reference internal" href="using-ggd.html">Using GGD</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">GGD Commands</a><ul>
<li class="toctree-l2"><a class="reference internal" href="ggd-search.html">ggd search</a></li>
<li class="toctree-l2"><a class="reference internal" href="install.html">ggd install</a></li>
<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="make-recipe.html">ggd make-recipe</a></li>
<li class="toctree-l2"><a class="reference internal" href="make-metarecipe.html">ggd make-meta-recipe</a></li>
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<div class="section" id="ggd-commands">
<span id="ggd-cli-page"></span><h1>GGD Commands<a class="headerlink" href="#ggd-commands" title="Permalink to this headline">¶</a></h1>
<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>
<p><strong>To see and/or search for data packages available through GGD, see:</strong> <a class="reference internal" href="recipes.html#recipes"><span class="std std-ref">Available data packages</span></a></p>
<div class="admonition important">
<p class="admonition-title">Important</p>
<p>If you use GGD, please cite the <a class="reference external" href="https://www.nature.com/articles/s41467-021-22381-z">Nature Communications GGD paper</a></p>
</div>
<p>The ggd command line interface (cli) has multiple tools for data access and local management. Below you can find a short
description of each tool, as well as links to specific pages about each.</p>
<p>Tabs for each tool are also available on the left tab bar.</p>
<table class="docutils align-default">
<colgroup>
<col style="width: 43%" />
<col style="width: 57%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Command</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p><a class="reference internal" href="ggd-search.html#ggd-search"><span class="std std-ref">ggd search</span></a></p></td>
<td><p>Search for a ggd data package</p></td>
</tr>
<tr class="row-odd"><td><p><a class="reference internal" href="predict-path.html#ggd-predict-path"><span class="std std-ref">ggd predict-path</span></a></p></td>
<td><p>Predict the file path of a data package that has not been
installed yet (Good for workflows like Snakemake)</p></td>
</tr>
<tr class="row-even"><td><p><a class="reference internal" href="install.html#ggd-install"><span class="std std-ref">ggd install</span></a></p></td>
<td><p>Install ggd data package(s)</p></td>
</tr>
<tr class="row-odd"><td><p><a class="reference internal" href="uninstall.html#ggd-uninstall"><span class="std std-ref">ggd uninstall</span></a></p></td>
<td><p>Uninstall a ggd data package(s)</p></td>
</tr>
<tr class="row-even"><td><p><a class="reference internal" href="list.html#ggd-list"><span class="std std-ref">ggd list</span></a></p></td>
<td><p>List the installed data packages (in a specific environment)</p></td>
</tr>
<tr class="row-odd"><td><p><a class="reference internal" href="list-file.html#ggd-get-files"><span class="std std-ref">ggd get-files</span></a></p></td>
<td><p>get the files for an installed ggd package</p></td>
</tr>
<tr class="row-even"><td><p><a class="reference internal" href="pkg-info.html#ggd-pkg-info"><span class="std std-ref">ggd pkg-info</span></a></p></td>
<td><p>Show a specific ggd package’s info</p></td>
</tr>
<tr class="row-odd"><td><p><a class="reference internal" href="show-env.html#ggd-show-env"><span class="std std-ref">ggd show-env</span></a></p></td>
<td><p>Show the ggd specific environment variables</p></td>
</tr>
<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>
<td><p>Create a ggd recipe from a bash script</p></td>
</tr>
<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>
<td><p>Create a ggd meta-recipe from a single or group of script</p></td>
</tr>
<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>
<td><p>Check/test a ggd recipe</p></td>
</tr>
</tbody>
</table>
<p>Command links:</p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="ggd-search.html">ggd search</a><ul>
<li class="toctree-l2"><a class="reference internal" href="ggd-search.html#using-ggd-search">Using ggd search</a></li>
<li class="toctree-l2"><a class="reference internal" href="ggd-search.html#example">Example</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="install.html">ggd install</a><ul>
<li class="toctree-l2"><a class="reference internal" href="install.html#using-ggd-install">Using ggd install</a></li>
<li class="toctree-l2"><a class="reference internal" href="install.html#examples">Examples</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="predict-path.html">ggd predict-path</a><ul>
<li class="toctree-l2"><a class="reference internal" href="predict-path.html#using-ggd-predict-path">Using ggd predict-path</a></li>
<li class="toctree-l2"><a class="reference internal" href="predict-path.html#examples">Examples</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="uninstall.html">ggd uninstall</a><ul>
<li class="toctree-l2"><a class="reference internal" href="uninstall.html#using-ggd-uninstall">Using ggd uninstall</a></li>
<li class="toctree-l2"><a class="reference internal" href="uninstall.html#examples">Examples</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="list.html">ggd list</a><ul>
<li class="toctree-l2"><a class="reference internal" href="list.html#using-ggd-list">Using ggd list</a></li>
<li class="toctree-l2"><a class="reference internal" href="list.html#examples">Examples</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="list-file.html">ggd get-files</a><ul>
<li class="toctree-l2"><a class="reference internal" href="list-file.html#using-ggd-get-files">Using ggd get-files</a></li>
<li class="toctree-l2"><a class="reference internal" href="list-file.html#examples">Examples</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pkg-info.html">ggd pkg-info</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pkg-info.html#using-ggd-pkg-info">Using ggd pkg-info</a></li>
<li class="toctree-l2"><a class="reference internal" href="pkg-info.html#examples">Examples</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="show-env.html">ggd show-env</a><ul>
<li class="toctree-l2"><a class="reference internal" href="show-env.html#using-ggd-show-env">Using ggd show-env</a></li>
<li class="toctree-l2"><a class="reference internal" href="show-env.html#examples">Examples</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="make-recipe.html">ggd make-recipe</a><ul>
<li class="toctree-l2"><a class="reference internal" href="make-recipe.html#using-ggd-make-recipe">Using ggd make-recipe</a></li>
<li class="toctree-l2"><a class="reference internal" href="make-recipe.html#data-recipe-standards">Data recipe standards</a></li>
<li class="toctree-l2"><a class="reference internal" href="make-recipe.html#examples">Examples</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="make-metarecipe.html">ggd make-meta-recipe</a><ul>
<li class="toctree-l2"><a class="reference internal" href="make-metarecipe.html#using-ggd-make-meta-recipe">Using ggd make-meta-recipe</a></li>
<li class="toctree-l2"><a class="reference internal" href="make-metarecipe.html#examples">Examples</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="check-recipe.html">ggd check-recipe</a><ul>
<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>
<li class="toctree-l2"><a class="reference internal" href="check-recipe.html#using-ggd-check-recipe">Using ggd check-recipe</a></li>
<li class="toctree-l2"><a class="reference internal" href="check-recipe.html#example">Example</a></li>
</ul>
</li>
</ul>
</div>
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