# HG changeset patch
# User yhoogstrate
# Date 1416409366 18000
# Node ID ddbaf017720aceaef749b36c931ed8412fa3fb30
# Parent  b871a8ea7d5bb7f47ea5b3218db6402b23cc5baf
Uploaded

diff -r b871a8ea7d5b -r ddbaf017720a README.rst
--- a/README.rst	Thu Nov 13 16:48:50 2014 -0500
+++ b/README.rst	Wed Nov 19 10:02:46 2014 -0500
@@ -1,7 +1,7 @@
 VarScan2 mpileup2snp wrapper for Galaxy
 =======================================
 
-<http://sourceforge.net/projects/varscan/>
+http://sourceforge.net/projects/varscan/
 
 This wrapper is optimized for direct access to BAM files such that the
 big mpileup files are not saved.
@@ -11,32 +11,28 @@
 
 * Repository-Maintainer: Youri Hoogstrate
 
-* Repository-Development: <https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools>
+* Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
 
 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
 Medical Center (Rotterdam, Netherlands) on behalf of the Translational
 Research IT (TraIT) project:
 
-<http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch>
+http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
 
 More tools by the Translational Research IT (TraIT) project can be found in the following repository:
 
-<http://toolshed.dtls.nl/>
+http://toolshed.dtls.nl/
 
 License
 -------
 
 **VarScan2**:
 
-Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0)
-
-<http://sourceforge.net/directory/os:linux/license:nposl3/freshness:recently-updated/>
-
-<http://opensource.org/licenses/NPOSL-3.0>
+Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0): http://sourceforge.net/directory/os:linux/license:nposl3/freshness:recently-updated/ http://opensource.org/licenses/NPOSL-3.0
 
 **samtools**:
 
-<https://raw.githubusercontent.com/samtools/samtools/develop/LICENSE>
+MIT/Expat License: https://raw.githubusercontent.com/samtools/samtools/develop/LICENSE
 
     The MIT/Expat License
 
@@ -73,22 +69,22 @@
 
 **samtools-parallel-mpileup**:
 
-<https://raw.githubusercontent.com/mydatascience/parallel-mpileup/master/samtools-0.1.19/COPYING>
+MIT License: https://raw.githubusercontent.com/mydatascience/parallel-mpileup/master/samtools-0.1.19/COPYING
 
-The MIT License
-
+    MIT License:
+    
     Copyright (c) 2008-2009 Genome Research Ltd.
-
+    
     Permission is hereby granted, free of charge, to any person obtaining a copy
     of this software and associated documentation files (the "Software"), to deal
     in the Software without restriction, including without limitation the rights
     to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
     copies of the Software, and to permit persons to whom the Software is
     furnished to do so, subject to the following conditions:
-
+    
     The above copyright notice and this permission notice shall be included in
     all copies or substantial portions of the Software.
-
+    
     THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
     IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
     FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
diff -r b871a8ea7d5b -r ddbaf017720a tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 13 16:48:50 2014 -0500
+++ b/tool_dependencies.xml	Wed Nov 19 10:02:46 2014 -0500
@@ -1,9 +1,8 @@
 <?xml version="1.0"?>
 <tool_dependency>
-	
 	<!--
 	<package name="ncurses" version="5.9">
-		<repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+		<repository name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" />
 	</package>
 	-->
 	
diff -r b871a8ea7d5b -r ddbaf017720a varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml	Thu Nov 13 16:48:50 2014 -0500
+++ b/varscan_mpileup2snp_from_bam.xml	Wed Nov 19 10:02:46 2014 -0500
@@ -85,6 +85,9 @@
 				#end if
 			#end if
 			
+			## Make for every MPILEUP file an 
+			## http://en.wikipedia.org/wiki/Named_pipe
+			
 			 | java
 					 -Xmx64G
 					 -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar