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<div class="section" id="ggd-show-env">
<span id="id1"></span><h1>ggd show-env<a class="headerlink" href="#ggd-show-env" 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><code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">show-env</span></code> is a tool used to show the ggd data package environment variables created during package installation
for the current conda environment.</p>
<p>During installation, ggd will place the processed files in a specific location on your system. To access
these files ggd creates up to two environment variables for each data package within a specific conda environment.
These variables contain either the directory path to the processed files or the file path to the main data file.
You can use <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">get-files</span></code> or <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">pkg-info</span></code> to find additional file paths for a ggd data
package, however, these environment variables provide quick access to the processed files without having to know
the file paths.</p>
<p>For details on using these environment variables in your analysis scripts see: <span class="xref std std-ref">Using installed data</span>.</p>
<div class="section" id="using-ggd-show-env">
<h2>Using ggd show-env<a class="headerlink" href="#using-ggd-show-env" title="Permalink to this headline">¶</a></h2>
<p>You can use ggd show-env to get a list of ggd data package environment variables.
Running <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">show-env</span> <span class="pre">-h</span></code> will give you the following message:</p>
<p>show-env arguments:</p>
<table class="docutils align-default">
<colgroup>
<col style="width: 22%" />
<col style="width: 78%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>ggd show-env</p></th>
<th class="head"><p>Display the environment variables for data packages installed in the current
conda 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) Regular expression pattern to match the name of the variable desired</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>There are no required arguments for using <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">show-env</span></code>, however, you can refine the results using
the <code class="code docutils literal notranslate"><span class="pre">-p</span></code> flag.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>Environment variables ending with <cite>_dir</cite> point to the directory path of the installed data package.</p>
<p>Environment variables ending with <cite>_file</cite> point to the main file from the installed data package.</p>
</div>
</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="id2">
<h3>1. Using ggd show-env<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h3>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd show-env
*****************************
Active environment variables:
> <span class="nv">$ggd_hg19_repeatmasker_ucsc_v1_dir</span>
> <span class="nv">$ggd_hg19_repeatmasker_ucsc_v1_file</span>
> <span class="nv">$ggd_grch37_esp_variants_ensembl_v1_dir</span>
> <span class="nv">$ggd_grch37_esp_variants_ensembl_v1_file</span>
> <span class="nv">$ggd_hg38_repeatmasker_ucsc_v1_dir</span>
> <span class="nv">$ggd_hg38_repeatmasker_ucsc_v1_file</span>
> <span class="nv">$ggd_grch37_reference_genome_ensembl_v1_dir</span>
> <span class="nv">$ggd_grch37_reference_genome_ensembl_v1_file</span>
> <span class="nv">$ggd_hg19_phastcons_ucsc_v1_dir</span>
> <span class="nv">$ggd_hg19_phastcons_ucsc_v1_file</span>
> <span class="nv">$ggd_hg19_gaps_ucsc_v1_dir</span>
> <span class="nv">$ggd_hg19_gaps_ucsc_v1_file</span>
> <span class="nv">$ggd_hg38_simplerepeats_ucsc_v1_dir</span>
> <span class="nv">$ggd_hg38_simplerepeats_ucsc_v1_file</span>
> <span class="nv">$ggd_hg19_simplerepeats_ucsc_v1_dir</span>
> <span class="nv">$ggd_hg19_simplerepeats_ucsc_v1_file</span>
.
.
.
*****************************
</pre></div>
</div>
</div>
<div class="section" id="using-the-p-flag">
<h3>2. Using the <cite>-p</cite> flag<a class="headerlink" href="#using-the-p-flag" title="Permalink to this headline">¶</a></h3>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd show-env -p ggd_hg19
*****************************
Active environment variables:
> <span class="nv">$ggd_hg19_phastcons_ucsc_v1_dir</span>
> <span class="nv">$ggd_hg19_phastcons_ucsc_v1_file</span>
> <span class="nv">$ggd_hg19_gaps_ucsc_v1_dir</span>
> <span class="nv">$ggd_hg19_gaps_ucsc_v1_file</span>
> <span class="nv">$ggd_hg19_repeatmasker_ucsc_v1_dir</span>
> <span class="nv">$ggd_hg19_repeatmasker_ucsc_v1_file</span>
> <span class="nv">$ggd_hg19_simplerepeats_ucsc_v1_dir</span>
> <span class="nv">$ggd_hg19_simplerepeats_ucsc_v1_file</span>
.
.
.
*****************************
</pre></div>
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