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    <title>Ragout - installation</title>
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          <h1>Ragout</h1>
          <h2>Chromosome assembly using multiple references</h2>
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<h1><a id="Installation_Instructions_for_Ragout_0"></a>Installation Instructions for Ragout</h1>
<h2><a id="Availability_3"></a>Availability</h2>
<p>Ragout is available for Mac OS and Linux.</p>
<h2><a id="Build_Requirements_8"></a>Build Requirements</h2>
<ul>
<li>C++ compiler with C++0x support (GCC 4.6+ / Clang 3.2+ / Apple Clang 4.2+)</li>
<li>GNU make / Cmake (for building Sibelia)</li>
</ul>
<h2><a id="Runtime_Depenencies_14"></a>Runtime Depenencies</h2>
<ul>
<li>Python 2.7</li>
<li>Sibelia [<a href="http://github.com/bioinf/Sibelia">http://github.com/bioinf/Sibelia</a>] or HAL Tools [<a href="https://github.com/glennhickey/hal">https://github.com/glennhickey/hal</a>]</li>
</ul>
<h2><a id="Binary_Distribution_21"></a>Binary Distribution</h2>
<p>Pre-compiled binaries are available for Linux and Mac OS from
the releases page [<a href="https://github.com/fenderglass/Ragout/releases">https://github.com/fenderglass/Ragout/releases</a>].
In this case you will not need the installation procedures below.</p>
<h2><a id="Building_29"></a>Building</h2>
<p>To build Ragout native modules, type:</p>
<pre><code>    make
</code></pre>
<p>You will also need either <em>Sibelia</em> or <em>HAL tools</em> installed (see below)</p>
<h2><a id="Sibelia_39"></a>Sibelia</h2>
<p>To build and install Sibelia, use:</p>
<pre><code>    python scripts/install-sibelia.py
</code></pre>
<p>If you already have Sieblia installed into your system, it will
be picked up automatically by Ragout.</p>
<h2><a id="HAL_Tools_50"></a>HAL Tools</h2>
<p>HAL alignment produced by <em>Progressive Cactus</em> could be used for synteny
blocks decomposition instead of <em>Sibelia</em> (recommended for large genomes).
If you want to use HAL alignment as input,
you need to install <em>HAL Tools</em> package [<a href="https://github.com/glennhickey/hal">https://github.com/glennhickey/hal</a>]
as it is described in the manual. Do not forget to properly set PATH and PYTHONPATH
environment variables.</p>
<h2><a id="Troubleshooting_61"></a>Troubleshooting</h2>
<p>Q: Many compilation errors, possibly with
“unrecognized command line option ‘-std=c++0x’” message:</p>
<p>A: Probably your compiler is too old and does not support C++0x. Minimum required
versions of GCC and Clang are given in the beginning of this document.</p>
<p>Q: “libstdc++.so.6: version `CXXABI_1.3.5’ not found” or similar error when running</p>
<p>A: Ensure that the version of libc++ that was used to compile Ragout is similar
to one the you currently using. You can specify an extra search path
to a specific library by setting “LD_LIBRARY_PATH” variable.</p>

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