Mercurial > repos > abossers > mummer_toolsuite
comparison MUMmer/README_mummer @ 0:6753195df9e0 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
| author | abossers |
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| date | Tue, 07 Jun 2011 17:49:58 -0400 |
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| -1:000000000000 | 0:6753195df9e0 |
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| 1 # Created/shared May 2011 | |
| 2 # | |
| 3 # Alex Bossers | |
| 4 # Central Veterinary Institute | |
| 5 # Wageningen University and Research centre | |
| 6 # Lelystad, The Netherlands | |
| 7 # | |
| 8 # Comments/improvements/bugs: Alex (dot) Bossers (at) wur (dot) nl | |
| 9 | |
| 10 | |
| 11 # WHAT IT DOES | |
| 12 The MUMmer suite is a set of very basic wrappers for the MUMmer genome comparison tools. Most common operations should be possible | |
| 13 by using these wrappers. MUMmer works fast on smaller (bacterial) genomes but can also cope with eukaryotic genomes. | |
| 14 | |
| 15 In addition to the original MUMmer tools it also contains an additional conversion script to convert MUMmer comparison files, | |
| 16 the so-called coords files into a readible format for Artemis Comparison Tool (ACT; Sanger UK). | |
| 17 | |
| 18 | |
| 19 # REQUIREMENTS | |
| 20 - Perl | |
| 21 - Galaxy :) | |
| 22 - MUMmer newer than version 3.20; | |
| 23 even though older versions might work as well. | |
| 24 Get your MUMmer here: http://mummer.sourceforge.net/ | |
| 25 Make sure MUMmer is in your PATH and/or update the tool xml configs and wrappers for the full MUMmer path | |
| 26 if it is different from /opt/MUMmer/MUMmer. | |
| 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 | |
| 28 - GNUplot is a requirement for the MUMmerplot part (see MUMmer installation documentation) | |
| 29 | |
| 30 | |
| 31 # SETUP | |
| 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 | |
| 33 of your galaxy instance and refresh the tools or restart the galaxy server. | |
| 34 | |
| 35 | |
| 36 # TESTING | |
| 37 You can test the code by running Nucmer on the test data and visualise the results in MUMmerplot. | |
| 38 It should return a MUMmerplot identical to the image provided. For reference I also included the corresponding log file. | |
| 39 | |
| 40 | |
| 41 # LICENSE | |
| 42 Copyright (c) 2011 Central Veterinary Institute of Wageningen UR, Lelystad, The Netherlands. | |
| 43 MUMmer is copyright by its respective owner. See their licensing details. | |
| 44 | |
| 45 Our wrappers/programs are free software; you can redistribute it and/or modify | |
| 46 it under the terms of the GNU General Public License as published by | |
| 47 the Free Software Foundation; either version 3 of the License, or | |
| 48 (at your option) any later version. | |
| 49 | |
| 50 When distributing the tools please include this original reference. | |
| 51 | |
| 52 Use this tool at your own risk. Even though we tried to build tools and wrappers that free of errors, | |
| 53 check your output since it might be erroneous. We will not be relyable to any failure this may have caused. | |
| 54 | |
| 55 If you like these scripts, please acknowledge our work. | |
| 56 |