annotate MUMmer/README_mummer @ 0:6753195df9e0 default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

# Created/shared May 2011
#
# Alex Bossers
# Central Veterinary Institute
# Wageningen University and Research centre
# Lelystad, The Netherlands
#
# Comments/improvements/bugs: Alex (dot) Bossers (at) wur (dot) nl


# WHAT IT DOES
The MUMmer suite is a set of very basic wrappers for the MUMmer genome comparison tools. Most common operations should be possible
by using these wrappers. MUMmer works fast on smaller (bacterial) genomes but can also cope with eukaryotic genomes.

In addition to the original MUMmer tools it also contains an additional conversion script to convert MUMmer comparison files,
the so-called coords files into a readible format for Artemis Comparison Tool (ACT; Sanger UK).


# REQUIREMENTS 
- Perl
- Galaxy :)
- MUMmer newer than version 3.20;
      even though older versions might work as well.
      Get your MUMmer here: http://mummer.sourceforge.net/
      Make sure MUMmer is in your PATH and/or update the tool xml configs and wrappers for the full MUMmer path
      if it is different from /opt/MUMmer/MUMmer.
- 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
- GNUplot is a requirement for the MUMmerplot part (see MUMmer installation documentation)


# SETUP 
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
of your galaxy instance and refresh the tools or restart the galaxy server.


# TESTING
You can test the code by running Nucmer on the test data and visualise the results in MUMmerplot. 
It should return a MUMmerplot identical to the image provided. For reference I also included the corresponding log file.


# LICENSE
Copyright (c) 2011 Central Veterinary Institute of Wageningen UR, Lelystad, The Netherlands.
MUMmer is copyright by its respective owner. See their licensing details.

Our wrappers/programs are free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
(at your option) any later version.

When distributing the tools please include this original reference.

Use this tool at your own risk. Even though we tried to build tools and wrappers that free of errors,
check your output since it might be erroneous. We will not be relyable to any failure this may have caused.

If you like these scripts, please acknowledge our work.