diff README @ 11:b22f8634ff84 draft

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty

--- a/README	Mon Jan 14 12:24:28 2013 -0600
+++ b/README	Sun Jan 17 14:11:06 2016 -0500
@@ -1,11 +1,12 @@
-The DeFuse galaxy tool is based on DeFuse_Version_0.6.0
+The DeFuse galaxy tool is based on DeFuse_Version_0.6.2
 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
+https://bitbucket.org/dranew/defuse
 
 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_0.6.0
+http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.2
 
 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.  
@@ -34,8 +35,13 @@
 
 These datasets should be referenced in the tool-data/defuse.loc file. 
 
+The create_reference_dataset will run the create_reference_dataset.pl script to generate deFuse genome reference data in a galaxy dataset.   
+This should me made available in the future as a Galaxy DataManager.
 
-External Tools  ( http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.0 )
+
+Galaxy will try to auto-install dependencies:
+
+External Tools  ( http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.2 )
 deFuse relies on other publically available tools as part of its pipeline. Some of these tools are not included with the deFuse download. Obtain these tools as detailed below.
 Download samtools
 The latest version of samtools can be downloaded from sourceforge: https://sourceforge.net/projects/samtools/files/samtools.