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install.html
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<title>Installation — PascalX 0.0.4 documentation</title>
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<section id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this heading"></a></h1>
<section id="multi-platform-docker">
<span id="dockersec"></span><h2>Multi-platform (Docker)<a class="headerlink" href="#multi-platform-docker" title="Permalink to this heading"></a></h2>
<p>Build a <a class="reference external" href="https://docker.com">Docker</a> image via</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">git</span> <span class="n">clone</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">BergmannLab</span><span class="o">/</span><span class="n">PascalX</span><span class="o">.</span><span class="n">git</span>
<span class="n">cd</span> <span class="n">PascalX</span>
<span class="n">docker</span> <span class="n">build</span> <span class="o">.</span> <span class="o">-</span><span class="n">t</span> <span class="n">pascalx</span><span class="p">:</span><span class="n">latest</span>
</pre></div>
</div>
<p>The image can be run in interactive mode with the host directory <code class="docutils literal notranslate"><span class="pre">/your/workdir</span></code> mounted as <code class="docutils literal notranslate"><span class="pre">/data</span></code> using the command</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">docker</span> <span class="n">run</span> <span class="o">--</span><span class="n">mount</span> <span class="n">src</span><span class="o">=/</span><span class="n">your</span><span class="o">/</span><span class="n">workdir</span><span class="p">,</span><span class="n">target</span><span class="o">=/</span><span class="n">data</span><span class="p">,</span><span class="nb">type</span><span class="o">=</span><span class="n">bind</span> <span class="o">-</span><span class="n">p</span> <span class="mi">8888</span><span class="p">:</span><span class="mi">8888</span> <span class="o">-</span><span class="n">it</span> <span class="n">pascalx</span> <span class="n">bash</span>
</pre></div>
</div>
<p>For data persistance after stopping the image, you should work exlusively in the <code class="docutils literal notranslate"><span class="pre">/data</span></code> directory.</p>
<p>A jupyter notebook running in the image can be started with</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">jupyter</span> <span class="n">notebook</span> <span class="o">--</span><span class="n">ip</span> <span class="mf">0.0.0.0</span> <span class="o">--</span><span class="n">allow</span><span class="o">-</span><span class="n">root</span>
</pre></div>
</div>
<p>Open on your host machine a browser and visit <a class="reference external" href="http://localhost:8888/">http://localhost:8888/</a> to use PascalX.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>You should allocate sufficient system resources to the docker runtime. A minimum of 8GB RAM should be made available. For making full use of parallel computation capabilities, at least 64GB of RAM is recommended. However, the precise numbers depend on the size of the GWAS and reference panel used.</p>
</div>
</section>
<section id="debian-ubuntu">
<h2>Debian/Ubuntu<a class="headerlink" href="#debian-ubuntu" title="Permalink to this heading"></a></h2>
<p>Use the <a class="reference external" href="https://docker.com">Docker</a> image or compile and install by yourself as follows:</p>
<dl class="simple">
<dt>Requirements:</dt><dd><ul class="simple">
<li><p>Python3 with development headers</p></li>
<li><p>GNU g++ with libquadmath, make</p></li>
<li><p><a class="reference external" href="https://www.boost.org">BOOST</a> libraries</p></li>
</ul>
</dd>
</dl>
<p>Install of requirements (for sudoers):</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">apt</span> <span class="n">install</span> <span class="n">python3</span> <span class="n">python3</span><span class="o">-</span><span class="n">dev</span> <span class="n">python3</span><span class="o">-</span><span class="n">setuptools</span> <span class="n">python3</span><span class="o">-</span><span class="n">pip</span> <span class="n">g</span><span class="o">++</span> <span class="n">make</span> <span class="n">libboost</span><span class="o">-</span><span class="nb">all</span><span class="o">-</span><span class="n">dev</span>
</pre></div>
</div>
<p>Set library path:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">export</span> <span class="n">LD_LIBRARY_PATH</span><span class="o">=</span><span class="s2">"/yourpath/PascalX/build/lib:$LD_LIBRARY_PATH"</span>
</pre></div>
</div>
<p>Or, as sudoer, add to <code class="docutils literal notranslate"><span class="pre">/etc/ld.so.conf.d/</span></code>.</p>
<p>Install of PascalX:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">git</span> <span class="n">clone</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">BergmannLab</span><span class="o">/</span><span class="n">PascalX</span><span class="o">.</span><span class="n">git</span>
<span class="n">cd</span> <span class="n">PascalX</span>
<span class="n">make</span> <span class="nb">all</span>
<span class="n">cd</span> <span class="n">python</span>
<span class="n">python3</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">install</span>
</pre></div>
</div>
</section>
<section id="mac">
<h2>Mac<a class="headerlink" href="#mac" title="Permalink to this heading"></a></h2>
<p>As the default LLVM compiler used by Xcode does not support quadmath at the time being, we recommend to use <a class="reference external" href="https://docker.com">Docker</a> on MacOS.</p>
</section>
<section id="windows">
<h2>Windows<a class="headerlink" href="#windows" title="Permalink to this heading"></a></h2>
<p>Please use the <a class="reference external" href="https://docker.com">Docker</a> image.</p>
</section>
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