The DeFuse galaxy tool is based on DeFuse_Version_0.4.2
  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 defuse source code is from: http://sourceforge.net/projects/defuse/files/defuse/0.4/defuse-0.4.2.tar.gz/download 
(without the defuse-0.4.2 dir level)
tar zxf defuse-0.4.2.tar.gz
cd tool 
make
cd ..

To use with non human genome references:
tar zxf modified_scripts.tgz
Defuse source was modified to include 2 extra parameters for non human references: gene_id_pattern and transcript_id_pattern
	scripts/alignjob.pl
	scripts/annotate_fusions.pl
	scripts/calculate_expression_simple.pl
	scripts/filter_bulk_fusion_reads.pl
	scripts/filter_sam_genes.pl
	scripts/find_concordant_ensembl.pl
	scripts/find_gene_clusters.pl


The defuse.xml galaxy tool wrapper will generate a defuse config.txt using values from tool-data/defuse.loc
and call scripts/defuse.pl