--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Thu Nov 10 09:56:05 2011 -0500
@@ -0,0 +1,29 @@
+The DeFuse galaxy tool is based on DeFuse_Version_0.4.3
+  http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
+
+DeFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion.
+
+
+Manual:
+  http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.3
+
+
+The included defuse source code is from:   http://sourceforge.net/projects/defuse/files/defuse/0.4/defuse-0.4.3.tar.gz/download 
+(to install uncompress the defuse source and navigate to the tools dir and type make)
+tar zxf defuse-0.4.3.tar.gz
+cd defuse-0.4.3/tool 
+make
+cd ../..
+
+Generate Reference Datasets as described in the Manual: 
+
+  The manual has detailed instructions on how to set up reference datasets for Human hg19 and hg18.  
+  We were able to follow the same basic procedures to set up a reference for Mouse mm9.
+
+  These datasets should be referenced in the tool-data/defuse.loc file.   
+
+
+The defuse.xml galaxy tool wrapper will generate a defuse config.txt using values from tool-data/defuse.loc
+and call defuse-0.4.3/scripts/defuse.pl
+
+