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_0.4.2

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 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.

These datasets should be referenced in the tool-data/defuse.loc file.