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<li><a class="reference internal" href="#running-prophyle-directly-from-the-repository">3.3. Running ProPhyle directly from the repository</a><ul>
<li><a class="reference internal" href="#adjusting-the-path-variable">Adjusting the PATH variable</a></li>
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<section id="installing-prophyle">
<span id="install"></span><h1><span class="section-number">3. </span>Installing ProPhyle<a class="headerlink" href="#installing-prophyle" title="Link to this heading">¶</a></h1>
<p>ProPhyle is written in Python, C and C++. It is distributed as a Python package
and all C/C++ programs are compiled upon the first execution
of the main program. ProPhyle requires a Unix operating system and the following dependencies:</p>
<ul class="simple">
<li><p>Python 3.3+ with the <a class="reference external" href="http://etetoolkit.org/">ETE3 library</a></p></li>
<li><p>GCC 4.8+</p></li>
<li><p>ZLib</p></li>
</ul>
<p>There are multiple ways of installation:</p>
<nav class="contents local" id="contents">
<ul class="simple">
<li><p><a class="reference internal" href="#installing-prophyle-using-bioconda" id="id1">Installing ProPhyle using Bioconda</a></p></li>
<li><p><a class="reference internal" href="#installing-prophyle-using-pip" id="id2">Installing ProPhyle using PIP</a></p></li>
<li><p><a class="reference internal" href="#running-prophyle-directly-from-the-repository" id="id3">Running ProPhyle directly from the repository</a></p></li>
</ul>
</nav>
<section id="installing-prophyle-using-bioconda">
<h2><span class="section-number">3.1. </span>Installing ProPhyle using Bioconda<a class="headerlink" href="#installing-prophyle-using-bioconda" title="Link to this heading">¶</a></h2>
<p>To set-up Bioconda, install
<a class="reference external" href="https://conda.io/miniconda.html">Miniconda</a>
or another Conda distribution, and
add <a class="reference external" href="https://bioconda.github.io/">Bioconda channels</a></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda<span class="w"> </span>config<span class="w"> </span>--add<span class="w"> </span>channels<span class="w"> </span>defaults
conda<span class="w"> </span>config<span class="w"> </span>--add<span class="w"> </span>channels<span class="w"> </span>conda-forge
conda<span class="w"> </span>config<span class="w"> </span>--add<span class="w"> </span>channels<span class="w"> </span>bioconda
</pre></div>
</div>
<p>You may either create a separate Conda environment
(which is the recommended approach)</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>prophyle<span class="w"> </span>prophyle
<span class="nb">source</span><span class="w"> </span>activate<span class="w"> </span>prophyle
</pre></div>
</div>
<p>or install ProPhyle directly to your main environment</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda<span class="w"> </span>install<span class="w"> </span>prophyle
</pre></div>
</div>
</section>
<section id="installing-prophyle-using-pip">
<h2><span class="section-number">3.2. </span>Installing ProPhyle using PIP<a class="headerlink" href="#installing-prophyle-using-pip" title="Link to this heading">¶</a></h2>
<p>There are three options of installing ProPhyle using PIP.</p>
<ol class="arabic">
<li><p>From PyPI</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>-U<span class="w"> </span>prophyle
</pre></div>
</div>
</div></blockquote>
</li>
<li><p>From Git</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>-U<span class="w"> </span>git+https://github.com/prophyle/prophyle
</pre></div>
</div>
</div></blockquote>
</li>
<li><p>From PyPI to the current directory</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>--user<span class="w"> </span>prophyle
<span class="nb">export</span><span class="w"> </span><span class="nv">PYTHONUSERBASE</span><span class="o">=</span><span class="sb">`</span><span class="nb">pwd</span><span class="sb">`</span>
<span class="nb">export</span><span class="w"> </span><span class="nv">PATH</span><span class="o">=</span><span class="nv">$PATH</span>:<span class="sb">`</span><span class="nb">pwd</span><span class="sb">`</span>/bin
</pre></div>
</div>
</div></blockquote>
</li>
</ol>
</section>
<section id="running-prophyle-directly-from-the-repository">
<h2><span class="section-number">3.3. </span>Running ProPhyle directly from the repository<a class="headerlink" href="#running-prophyle-directly-from-the-repository" title="Link to this heading">¶</a></h2>
<p>It also is possible to run ProPhyle directly from the repository, by calling
the main script</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prophyle/prophyle/prophyle.py
</pre></div>
</div>
<p>or its alias</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prophyle/prophyle/prophyle
</pre></div>
</div>
<p>ProPhyle will then automatically adjust all paths of the auxiliary programs.</p>
<p>Note that ProPhyle uses submodules, therefore the repository needs to
be clonned with the <cite>–recursive</cite> option</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>--recursive<span class="w"> </span>http://github.com/prophyle/prophyle
</pre></div>
</div>
<section id="adjusting-the-path-variable">
<h3>Adjusting the PATH variable<a class="headerlink" href="#adjusting-the-path-variable" title="Link to this heading">¶</a></h3>
<p>The ProPhyle path can be prepended to the <cite>$PATH</cite> variable so that ProPhyle
can be executed in the same way as if it was installed using PIP</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span><span class="w"> </span><span class="nv">PATH</span><span class="o">=</span><span class="k">$(</span><span class="nb">pwd</span><span class="k">)</span>/prophyle/prophyle:<span class="nv">$PATH</span>
</pre></div>
</div>
</section>
<section id="installing-dependencies">
<h3>Installing dependencies<a class="headerlink" href="#installing-dependencies" title="Link to this heading">¶</a></h3>
<p>When run from the repository,
some of the ProPhyle dependencies, listed in <cite>requirements.txt</cite>, might
be missing in the system.
It is possible to install them either using BioConda</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>cat<span class="w"> </span>prophyle/requirements.txt<span class="w"> </span><span class="p">|</span><span class="w"> </span>perl<span class="w"> </span>-pe<span class="w"> </span><span class="s1">'s/==.*//g'</span><span class="w"> </span><span class="p">|</span><span class="w"> </span>xargs<span class="w"> </span>conda<span class="w"> </span>install
</pre></div>
</div>
<p>or using PIP</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>cat<span class="w"> </span>prophyle/requirements.txt<span class="w"> </span><span class="p">|</span><span class="w"> </span>xargs<span class="w"> </span>pip<span class="w"> </span>install
</pre></div>
</div>
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