Mercurial > repos > abossers > mummer_toolsuite

annotate MUMmer/README_mummer @ 2:479eb076cd23

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add revised mummer toolshed files to testtoolshed
author abossers
date Tue, 28 Oct 2014 16:59:33 +0100
parents 59f302448cf6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
1 # Created/shared May 2011
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
2 #
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
3 # Alex Bossers
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
4 # Central Veterinary Institute
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
5 # Wageningen University and Research centre
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
6 # Lelystad, The Netherlands
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
7 #
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
8 # Comments/improvements/bugs: Alex (dot) Bossers (at) wur (dot) nl
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
9
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
10
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
11 # WHAT IT DOES
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
12 The MUMmer suite is a set of very basic wrappers for the MUMmer genome comparison tools. Most common operations should be possible
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
13 by using these wrappers. MUMmer works fast on smaller (bacterial) genomes but can also cope with eukaryotic genomes.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
14
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
15 In addition to the original MUMmer tools it also contains an additional conversion script to convert MUMmer comparison files,
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
16 the so-called coords files into a readible format for Artemis Comparison Tool (ACT; Sanger UK).
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
17
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
18
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
19 # REQUIREMENTS
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
20 - Perl
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
21 - Galaxy :)
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
22 - MUMmer newer than version 3.20;
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
23 even though older versions might work as well.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
24 Get your MUMmer here: http://mummer.sourceforge.net/
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
25 Make sure MUMmer is in your PATH and/or update the tool xml configs and wrappers for the full MUMmer path
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
26 if it is different from /opt/MUMmer/MUMmer.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
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
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
28 - GNUplot is a requirement for the MUMmerplot part (see MUMmer installation documentation)
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
29
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
30
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
31 # SETUP
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
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
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
33 of your galaxy instance and refresh the tools or restart the galaxy server.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
34
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
35
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
36 # TESTING
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
37 You can test the code by running Nucmer on the test data and visualise the results in MUMmerplot.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
38 It should return a MUMmerplot identical to the image provided. For reference I also included the corresponding log file.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
39
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
40
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
41 # LICENSE
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
42 Copyright (c) 2011 Central Veterinary Institute of Wageningen UR, Lelystad, The Netherlands.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
43 MUMmer is copyright by its respective owner. See their licensing details.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
44
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
45 Our wrappers/programs are free software; you can redistribute it and/or modify
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
46 it under the terms of the GNU General Public License as published by
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
47 the Free Software Foundation; either version 3 of the License, or
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
48 (at your option) any later version.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
49
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
50 When distributing the tools please include this original reference.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
51
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
52 Use this tool at your own risk. Even though we tried to build tools and wrappers that free of errors,
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
53 check your output since it might be erroneous. We will not be relyable to any failure this may have caused.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
54
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
55 If you like these scripts, please acknowledge our work.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
56