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GNUplot with PNG support
author abossers
date Wed, 29 Oct 2014 15:40:42 +0100
parents 59f302448cf6
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59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 # Created/shared May 2011
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2 #
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3 # Alex Bossers
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4 # Central Veterinary Institute
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5 # Wageningen University and Research centre
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6 # Lelystad, The Netherlands
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7 #
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8 # Comments/improvements/bugs: Alex (dot) Bossers (at) wur (dot) nl
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11 # WHAT IT DOES
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12 The MUMmer suite is a set of very basic wrappers for the MUMmer genome comparison tools. Most common operations should be possible
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13 by using these wrappers. MUMmer works fast on smaller (bacterial) genomes but can also cope with eukaryotic genomes.
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15 In addition to the original MUMmer tools it also contains an additional conversion script to convert MUMmer comparison files,
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16 the so-called coords files into a readible format for Artemis Comparison Tool (ACT; Sanger UK).
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19 # REQUIREMENTS
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20 - Perl
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21 - Galaxy :)
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22 - MUMmer newer than version 3.20;
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23 even though older versions might work as well.
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24 Get your MUMmer here: http://mummer.sourceforge.net/
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25 Make sure MUMmer is in your PATH and/or update the tool xml configs and wrappers for the full MUMmer path
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26 if it is different from /opt/MUMmer/MUMmer.
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27 - ACT can be run locally or via Webstart if you want to visualise genome comparisons in detail: http://www.sanger.ac.uk/resources/software/act
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28 - GNUplot is a requirement for the MUMmerplot part (see MUMmer installation documentation)
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31 # SETUP
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32 Just unpack the tool xml and perl script somewhere appropriate and adapt the MUMmer installation part if different from above. Plug the tool in the tool_config.xml
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33 of your galaxy instance and refresh the tools or restart the galaxy server.
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36 # TESTING
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37 You can test the code by running Nucmer on the test data and visualise the results in MUMmerplot.
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38 It should return a MUMmerplot identical to the image provided. For reference I also included the corresponding log file.
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41 # LICENSE
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42 Copyright (c) 2011 Central Veterinary Institute of Wageningen UR, Lelystad, The Netherlands.
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43 MUMmer is copyright by its respective owner. See their licensing details.
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45 Our wrappers/programs are free software; you can redistribute it and/or modify
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46 it under the terms of the GNU General Public License as published by
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47 the Free Software Foundation; either version 3 of the License, or
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48 (at your option) any later version.
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50 When distributing the tools please include this original reference.
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52 Use this tool at your own risk. Even though we tried to build tools and wrappers that free of errors,
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53 check your output since it might be erroneous. We will not be relyable to any failure this may have caused.
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55 If you like these scripts, please acknowledge our work.
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