Commit bb9c2c3a authored by Christian Arnold's avatar Christian Arnold

Documentation update

parent 1ddae0f9
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The following quick start briefly summarizes the necessary steps to use our pipeline:
1. Install the necessary tools (Snakemake, samtools, bedtools, and Subread).
.. note:: Note that they all require Python 3.
.. note:: Note that all tools require Python 3.
We recommend installing them via conda, in which case the installation is as easy as
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<blockquote>
<div><div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Note that they all require Python 3.</p>
<p class="last">Note that all tools require Python 3.</p>
</div>
<p>We recommend installing them via conda, in which case the installation is as easy as</p>
<div class="highlight-Bash"><div class="highlight"><pre><span></span>conda install -c bioconda snakemake bedtools samtools subread
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<li class="toctree-l2"><a class="reference internal" href="chapter2.html#input-metadata">Input metadata</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#output">Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#output">Output</a><ul>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#folder-final-output">FOLDER <code class="docutils literal"><span class="pre">FINAL_OUTPUT</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#folder-peaks">FOLDER <code class="docutils literal"><span class="pre">PEAKS</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#folder-tf-specific">FOLDER <code class="docutils literal"><span class="pre">TF-SPECIFIC</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#folder-logs-and-benchmarks">FOLDER <code class="docutils literal"><span class="pre">LOGS_AND_BENCHMARKS</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#folder-temp">FOLDER <code class="docutils literal"><span class="pre">TEMP</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#working-with-the-pipeline-and-frequently-asked-questions">Working with the pipeline and frequently asked questions</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#handling-errors">Handling errors</a><ul>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#error-types">Error types</a></li>
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