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<div class="section" id="ggd-list">
<span id="id1"></span><h1>ggd list<a class="headerlink" href="#ggd-list" 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>The <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">list</span></code> command is used to list the installed ggd data packages in a specific conda environment. This
command is similar to <code class="code docutils literal notranslate"><span class="pre">conda</span> <span class="pre">list</span></code>, but is specific for ggd data packages.</p>
<div class="section" id="using-ggd-list">
<h2>Using ggd list<a class="headerlink" href="#using-ggd-list" title="Permalink to this headline">¶</a></h2>
<p>Use <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">list</span></code> to list ggd data package installed in the current or specific conda environment.
Running <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">list</span> <span class="pre">-h</span></code> will give you the following message:</p>
<p>List arguments:</p>
<table class="docutils align-default">
<colgroup>
<col style="width: 29%" />
<col style="width: 71%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>ggd list</p></th>
<th class="head"><p>Get a list of ggd data packages installed in the current or
specified conda prefix/environment.</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">-h</span></code>, <code class="docutils literal notranslate"><span class="pre">--help</span></code></p></td>
<td><p>show this help message and exit</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">-p,</span></code> <code class="docutils literal notranslate"><span class="pre">--pattern</span></code></p></td>
<td><p>(Optional) pattern to match the name of the ggd data package.</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--prefix</span></code></p></td>
<td><p>(Optional) The name or the full directory path to a
conda environment where a ggd recipe is stored. (Only
needed if listing data files not in the current environment)</p></td>
</tr>
</tbody>
</table>
<div class="section" id="additional-argument-explanation">
<h3>Additional argument explanation:<a class="headerlink" href="#additional-argument-explanation" title="Permalink to this headline">¶</a></h3>
<p>Optional arguments:</p>
<ul class="simple">
<li><p><em>-p:</em> The <code class="code docutils literal notranslate"><span class="pre">-p</span></code> flag is used to list a specific installed data package. If <code class="code docutils literal notranslate"><span class="pre">-p</span></code> is not used, all installed data packages will be displayed.</p></li>
<li><p><em>–prefix:</em> <code class="code docutils literal notranslate"><span class="pre">--prefix</span></code> flag is used to list the installed data packages for a specific conda environment/prefix. If not set
the data packages for the current environment will be listed</p></li>
</ul>
</div>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="section" id="list-all-installed-data-packages">
<h3>1. List all installed data packages:<a class="headerlink" href="#list-all-installed-data-packages" title="Permalink to this headline">¶</a></h3>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd list
<span class="c1"># Packages in environment: <env></span>
<span class="c1">#</span>
------------------------------------------------------------------------------------------------------------------------
Name Pkg-Version Pkg-Build Channel Environment-Variables
------------------------------------------------------------------------------------------------------------------------
-> grch37-haploinsufficient-genes-clingen-v1 <span class="m">1</span> <span class="m">1</span> ggd-genomics <span class="nv">$ggd_grch37_haploinsufficient_genes_clingen_v1_dir</span>
-> hg19-chromsizes-ggd-v1 <span class="m">1</span> <span class="m">1</span> ggd-genomics <span class="nv">$ggd_hg19_chromsizes_ggd_v1_dir</span>, <span class="nv">$ggd_hg19_chromsizes_ggd_v1_file</span>
-> hg19-gaps-ucsc-v1 <span class="m">1</span> <span class="m">1</span> ggd-genomics <span class="nv">$ggd_hg19_gaps_ucsc_v1_dir</span>, <span class="nv">$ggd_hg19_gaps_ucsc_v1_file</span>
...
<span class="c1"># To use the environment variables run `source activate base`</span>
<span class="c1"># You can see the available ggd data package environment variables by running `ggd show-env`</span>
</pre></div>
</div>
</div>
<div class="section" id="list-a-specific-installed-data-package-using-a-pattern">
<h3>2. List a specific installed data package using a pattern:<a class="headerlink" href="#list-a-specific-installed-data-package-using-a-pattern" title="Permalink to this headline">¶</a></h3>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd list -p chromsizes
<span class="c1"># Packages in environment: <env></span>
<span class="c1">#</span>
------------------------------------------------------------------------------------------------------------------------
Name Pkg-Version Pkg-Build Channel Environment-Variables
------------------------------------------------------------------------------------------------------------------------
-> hg19-chromsizes-ggd-v1 <span class="m">1</span> <span class="m">1</span> ggd-genomics <span class="nv">$ggd_hg19_chromsizes_ggd_v1_dir</span>, <span class="nv">$ggd_hg19_chromsizes_ggd_v1_file</span>
<span class="c1"># To use the environment variables run `source activate base`</span>
<span class="c1"># You can see the available ggd data package environment variables by running `ggd show-env`</span>
</pre></div>
</div>
</div>
<div class="section" id="list-installed-packages-in-a-different-prefix">
<h3>3. List installed packages in a different prefix:<a class="headerlink" href="#list-installed-packages-in-a-different-prefix" title="Permalink to this headline">¶</a></h3>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd list --prefix data
<span class="c1"># Packages in environment: <data environment></span>
<span class="c1">#</span>
------------------------------------------------------------------------------------------------------------------------
Name Pkg-Version Pkg-Build Channel Environment-Variables
------------------------------------------------------------------------------------------------------------------------
-> grch37-chromsizes-ggd-v1 <span class="m">1</span> <span class="m">1</span> ggd-genomics <span class="nv">$ggd_grch37_chromsizes_ggd_v1_dir</span>, <span class="nv">$ggd_grch37_chromsizes_ggd_v1_file</span>
-> grch37-eiee-genes-ostrander-v1 <span class="m">1</span> <span class="m">1</span> ggd-genomics <span class="nv">$ggd_grch37_eiee_genes_ostrander_v1_dir</span>
-> grch37-microsatellites-ucsc-v1 <span class="m">1</span> <span class="m">1</span> ggd-genomics <span class="nv">$ggd_grch37_microsatellites_ucsc_v1_dir</span>, <span class="nv">$ggd_grch37_microsatellites_ucsc_v1_file</span>
...
<span class="c1"># The environment variables are only available when you are using the '<data environment>' conda environment.</span>
</pre></div>
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