--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MUMmer/README_mummer	Tue Mar 31 14:19:49 2015 +0200
@@ -0,0 +1,56 @@
+# 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.
+