--- a/README	Fri Jan 06 16:06:17 2012 -0600
+++ b/README	Fri Jan 04 13:29:03 2013 -0600
@@ -1,29 +1,35 @@
-The DeFuse galaxy tool is based on DeFuse_Version_0.4.3
-  http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
+The DeFuse galaxy tool is based on DeFuse_Version_0.5.0
+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
+http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2
+
+The included tool_dependencies.xml will download and install the defuse code.  
+It will set the environment variable: "DEFUSE_PATH" to the location of the defuse install.  
 
 
-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 ../..
+The defuse.pl command relies on a configuration file to specifiy options, the location of reference data, and other applications that it depends upon: bowtie, bowtie-build, samtools, blat, fatotwobit, R, and Rscript.
+
+The DeFuse galaxy tool can either construct the config.txt file that is mentioned in the defuse manual, or select an existing config.txt file in the users history.   
+When constructing the config.txt file, the DeFuse tool uses the values selected in: tool-data/defuse.loc    
+The dictionary field in the tool-data/defuse.loc can be used to set fields in the config.txt file, including the site specific location of reference data and the paths to the other application binaries.  
+The "Defuse parameter settings" are used to alter options in the config.txt file.
+
+The DeFuse galaxy tool also generates a bash script to run defuse.  
+That script will attempt to edit the config.txt file to specifiy any unset paths to applications that defuse relies upon:
+bowtie, bowtie-build, samtools, blat, fatotwobit, R, and Rscript
+The script uses the using the shell "which" command to discover the application path, so the required applications should in PATH environment variable.
+
 
 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.
+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.   
+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
 
-