diff README @ 0:b75ea9927793

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+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. 
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