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<?xml version="1.0" ?>
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<title>generate_graph.pl</title>
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	<li><a href="#name">NAME</a></li>
	<li><a href="#synopsis">SYNOPSIS</a></li>
	<li><a href="#description">DESCRIPTION</a></li>
	<li><a href="#options">OPTIONS</a></li>
	<li><a href="#external_dependencies">EXTERNAL DEPENDENCIES</a></li>
	<li><a href="#license">LICENSE</a></li>
	<li><a href="#contact">CONTACT</a></li>
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<p>
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<h1><a name="name">NAME</a></h1>
<pre>
    generate_graph.pl</pre>
<p>
</p>
<hr />
<h1><a name="synopsis">SYNOPSIS</a></h1>
<pre>
    ./generate_graph.pl [ -url mysql://user:pass@server:port/dbname ] [-pipeconfig TopUp_conf.pm]* -output OUTPUT_LOC [-help]</pre>
<p>
</p>
<hr />
<h1><a name="description">DESCRIPTION</a></h1>
<pre>
    This program will generate a graphical representation of your hive pipeline.
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    This includes visalising the flow of data from the different analyses, blocking
    rules &amp; table writers. The graph is also coloured to indicate the stage
    an analysis is at. The colours &amp; fonts used can be configured via
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    hive_config.json configuration file.</pre>
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</p>
<hr />
<h1><a name="options">OPTIONS</a></h1>
<p><strong>--url</strong></p>
<pre>
    url defining where hive database is located</pre>
<p><strong>--reg_conf</strong></p>
<pre>
    path to a Registry configuration file</pre>
<p><strong>--reg_alias</strong></p>
<pre>
    species/alias name for the Hive DBAdaptor</pre>
<p><strong>--pipeconfig</strong></p>
<pre>
    A pipeline configuration file that can function both as the initial source of pipeline structure or as a top-up config.
    This option can now be used multiple times for multiple top-ups.</pre>
<p><strong>--output</strong></p>
<pre>
    Location of the file to write to.
    The file extension (.png , .jpeg , .dot , .gif , .ps) will define the output format.</pre>
<p>
</p>
<hr />
<h1><a name="external_dependencies">EXTERNAL DEPENDENCIES</a></h1>
<pre>
    GraphViz</pre>
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</p>
<hr />
<h1><a name="license">LICENSE</a></h1>
<pre>
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    Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute</pre>
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<pre>
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    Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License.
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    You may obtain a copy of the License at</pre>
<pre>
         <a href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a></pre>
<pre>
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    Unless required by applicable law or agreed to in writing, software distributed under the License
    is distributed on an &quot;AS IS&quot; BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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    See the License for the specific language governing permissions and limitations under the License.</pre>
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</p>
<hr />
<h1><a name="contact">CONTACT</a></h1>
<pre>
    Please subscribe to the Hive mailing list:  <a href="http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users">http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users</a>  to discuss Hive-related questions or to be notified of our updates</pre>
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