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<div class="section" id="quick-installation">
<span id="quick-install"></span><h1>Quick installation<a class="headerlink" href="#quick-installation" title="Permalink to this headline">¶</a></h1>
<div class="section" id="pycogent-app-for-osx-10-6">
<h2>PyCogent.app for OSX 10.6<a class="headerlink" href="#pycogent-app-for-osx-10-6" title="Permalink to this headline">¶</a></h2>
<p><a class="reference external" href="http://sourceforge.net/projects/pycogent/files/PyCogent.app/">Download PyCogent.app</a>. This native OSX app comes bundled with all required dependencies and is a download, decompress and go experience! It also implements the novel script form system that controls command line scripts via a form based input mechanism.</p>
</div>
<div class="section" id="by-virtual-machine">
<h2>By virtual machine<a class="headerlink" href="#by-virtual-machine" title="Permalink to this headline">¶</a></h2>
<p>One way to install PyCogent is to install the QIIME virtual machine using VirtualBox. The installation instructions can be found <a class="reference external" href="http://qiime.sourceforge.net/install/virtual_box.html">here</a>. As QIIME does not yet support the latest version of matplotlib, some PyCogent drawing capabilities are broken.</p>
<p>Please, note that this is the only installation method supported for Windows and that natively Windows does not support gz files properly so to uncompress a gz file in Windows use <a class="reference external" href="http://www.7-zip.org/">7-zip</a>.</p>
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<div class="section" id="for-systems-with-easy-install">
<h2>For systems with <tt class="docutils literal"><span class="pre">easy_install</span></tt><a class="headerlink" href="#for-systems-with-easy-install" title="Permalink to this headline">¶</a></h2>
<p>For the list of dependencies see the <a class="reference internal" href="README.html#required"><em>Required</em></a> software list.</p>
<p>The following assumes you have <tt class="docutils literal"><span class="pre">easy_install</span></tt> on your system (this comes standard with new Mac’s for instance), that you have administrator privileges and that you’re connected to the internet. See below if you don’t have <tt class="docutils literal"><span class="pre">easy_install</span></tt>.</p>
<p>The key steps for the minimal install are:</p>
<ol class="arabic">
<li><p class="first">Download the <a class="reference download internal" href="_downloads/cogent-requirements.txt"><tt class="xref download docutils literal"><span class="pre">requirements</span> <span class="pre">file</span></tt></a>.</p>
</li>
<li><p class="first">Install pip</p>
<div class="highlight-python"><pre>$ sudo easy_install -U pip</pre>
</div>
</li>
<li><p class="first">Use pip to download, build and install PyCogent plus the numpy dependency.</p>
<div class="highlight-python"><pre>$ DONT_USE_PYREX=1 sudo pip install -r path/to/cogent-requirements.txt</pre>
</div>
</li>
</ol>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The <tt class="docutils literal"><span class="pre">DONT_USE_PYREX=1</span></tt> statement is required if you have Pyrex installed due to a conflict between setuptools and later versions of Pyrex. If you don’t have Pyrex, this will still work.</p>
</div>
<p>If the above fails to download PyCogent you can <a class="reference external" href="http://sourceforge.net/projects/pycogent">download the tarball</a> to your hard drive and replace the first line of the <a class="reference download internal" href="_downloads/cogent-requirements.txt"><tt class="xref download docutils literal"><span class="pre">requirements</span> <span class="pre">file</span></tt></a> with the full path to the tarball, e.g. <tt class="docutils literal"><span class="pre">/Users/my_user_name/Downloads/cogent-1.4.tgz</span></tt>.</p>
<div class="section" id="optional-installs">
<h3>Optional installs<a class="headerlink" href="#optional-installs" title="Permalink to this headline">¶</a></h3>
<div class="section" id="to-use-the-ensembl-querying-code">
<h4>To use the Ensembl querying code<a class="headerlink" href="#to-use-the-ensembl-querying-code" title="Permalink to this headline">¶</a></h4>
<p>Add the following lines to the requirements file</p>
<div class="highlight-python"><pre>MySQL-python>=1.2.2
SQLAlchemy>=0.5</pre>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The MySQL-python module requires that you have MySQL installed.</p>
</div>
</div>
<div class="section" id="to-use-the-parallel-capabilities">
<h4>To use the parallel capabilities<a class="headerlink" href="#to-use-the-parallel-capabilities" title="Permalink to this headline">¶</a></h4>
<p>Add the following to the requirements file</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">mpi4py</span><span class="o">>=</span><span class="mf">1.0</span>
</pre></div>
</div>
</div>
<div class="section" id="to-build-the-documentation">
<h4>To build the documentation<a class="headerlink" href="#to-build-the-documentation" title="Permalink to this headline">¶</a></h4>
<p>Add the following to the requirements file</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">Sphinx</span><span class="o">>=</span><span class="mf">0.6</span>
</pre></div>
</div>
</div>
<div class="section" id="to-use-the-development-version-of-pycogent">
<h4>To use the development version of PyCogent<a class="headerlink" href="#to-use-the-development-version-of-pycogent" title="Permalink to this headline">¶</a></h4>
<p>Just replace the first line of the requirements file with <tt class="docutils literal"><span class="pre">https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk</span></tt>.</p>
</div>
<div class="section" id="to-use-the-graphics-capabilities">
<h4>To use the graphics capabilities<a class="headerlink" href="#to-use-the-graphics-capabilities" title="Permalink to this headline">¶</a></h4>
<p>You need to install <a class="reference external" href="http://matplotlib.sourceforge.net/">matplotlib</a> (version 0.99+) to use the drawing code. However, compiling matplotlib can be a challenge. We therefore suggest you obtain a prebuilt binary for your platform from the <a class="reference external" href="http://matplotlib.sourceforge.net/">matplotlib</a> project page rather than modify the requirements file. For OSX, we suggest reading the following instructions on how to <a class="reference external" href="http://bioinformatics.anu.edu.au/groups/huttleylab/wiki/da9fe/Building_matplotlib_for_Snow_Leopard.html">compiling matplotlib</a>.</p>
</div>
</div>
</div>
<div class="section" id="installing-easy-install">
<h2>Installing <tt class="docutils literal"><span class="pre">easy_install</span></tt><a class="headerlink" href="#installing-easy-install" title="Permalink to this headline">¶</a></h2>
<p>If your system doesn’t have <tt class="docutils literal"><span class="pre">easy_install</span></tt>, you can execute the following:</p>
<div class="highlight-python"><pre>$ sudo curl http://peak.telecommunity.com/dist/ez_setup.py | python</pre>
</div>
<p>or, if you are on a linux system that has a package manager, you may only need to do something like:</p>
<div class="highlight-python"><pre>$ sudo apt-get install python-setuptools</pre>
</div>
<p>Use the approach to getting <tt class="docutils literal"><span class="pre">easy_install</span></tt> that best suites your system, then follow the (above) instructions for the <tt class="docutils literal"><span class="pre">pip</span></tt> based installation.</p>
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<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Quick installation</a><ul>
<li><a class="reference internal" href="#pycogent-app-for-osx-10-6">PyCogent.app for OSX 10.6</a></li>
<li><a class="reference internal" href="#by-virtual-machine">By virtual machine</a></li>
<li><a class="reference internal" href="#for-systems-with-easy-install">For systems with <tt class="docutils literal"><span class="pre">easy_install</span></tt></a><ul>
<li><a class="reference internal" href="#optional-installs">Optional installs</a><ul>
<li><a class="reference internal" href="#to-use-the-ensembl-querying-code">To use the Ensembl querying code</a></li>
<li><a class="reference internal" href="#to-use-the-parallel-capabilities">To use the parallel capabilities</a></li>
<li><a class="reference internal" href="#to-build-the-documentation">To build the documentation</a></li>
<li><a class="reference internal" href="#to-use-the-development-version-of-pycogent">To use the development version of PyCogent</a></li>
<li><a class="reference internal" href="#to-use-the-graphics-capabilities">To use the graphics capabilities</a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#installing-easy-install">Installing <tt class="docutils literal"><span class="pre">easy_install</span></tt></a></li>
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