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install.html
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<title>Quick installation using pip — PyCogent 1.9 documentation</title>
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<div class="section" id="quick-installation-using-pip">
<span id="quick-install"></span><h1>Quick installation using pip<a class="headerlink" href="#quick-installation-using-pip" title="Permalink to this headline">¶</a></h1>
<p>The following assumes you have <code class="docutils literal"><span class="pre">pip</span></code> on your system (this comes standard with new Macs for instance), that you have made a <a class="reference external" href="https://pypi.python.org/pypi/virtualenv">virtualenv</a> or a <a class="reference external" href="http://conda.pydata.org/docs/">conda</a> environment and that you’re connected to the internet.</p>
<p>The key steps for the minimal install are:</p>
<ol class="arabic">
<li><p class="first">Install numpy</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ pip install numpy
</pre></div>
</div>
</li>
<li><p class="first">Use pip to download, build and install PyCogent.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ pip install cogent
</pre></div>
</div>
</li>
</ol>
<p>If the above fails to download PyCogent you can <a class="reference external" href="https://github.com/pycogent/pycogent">download an archive</a> to your hard drive and then do.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ pip install path/to/pycogent-master.zip
</pre></div>
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<div class="section" id="optional-installs">
<h2>Optional installs<a class="headerlink" href="#optional-installs" title="Permalink to this headline">¶</a></h2>
<div class="section" id="to-use-the-ensembl-querying-code">
<h3>To use the Ensembl querying code<a class="headerlink" href="#to-use-the-ensembl-querying-code" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div>$ pip install cogent[mysql]</div></blockquote>
</div>
<div class="section" id="to-use-the-parallel-capabilities">
<h3>To use the parallel capabilities<a class="headerlink" href="#to-use-the-parallel-capabilities" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div>$ pip install cogent[mpi]</div></blockquote>
</div>
<div class="section" id="to-install-all-dependencies">
<h3>To install all dependencies<a class="headerlink" href="#to-install-all-dependencies" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div>$ pip install cogent[all]</div></blockquote>
<p>This will install all the above and matplotlib for drawing</p>
</div>
<div class="section" id="to-use-the-development-version-of-pycogent">
<h3>To use the development version of PyCogent<a class="headerlink" href="#to-use-the-development-version-of-pycogent" title="Permalink to this headline">¶</a></h3>
<p>Just replace the first line of the requirements file with <code class="docutils literal"><span class="pre">git+https://github.com/pycogent/pycogent.git</span></code>.</p>
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<h3>Table Of Contents</h3>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Quick installation using pip</a></li>
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<li class="toctree-l1"><a class="reference internal" href="coding_guidelines.html">Coding guidelines</a></li>
<li class="toctree-l1"><a class="reference internal" href="data_file_links.html">The data files used in the documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="examples/index.html">Cogent Usage Examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="cookbook/index.html">PyCogent Cookbook</a></li>
<li class="toctree-l1"><a class="reference internal" href="developer_notes.html">For Developers</a></li>
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