# HG changeset patch
# User nilesh
# Date 1373305815 14400
# Node ID fc54556b7999ca20d83c6287a3864394f9434914
# Parent  ca5c13b3af0e71b7ed912a02a86a944bb25af9e1
Deleted selected files

diff -r ca5c13b3af0e -r fc54556b7999 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jul 08 13:43:28 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="somatic-sniper" version="unstable">
-        <install version="1.0">
-            <actions>
-
-                <!-- Samtools -->
-            	<action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.6/samtools-0.1.6.tar.bz2</action>
-                <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
-                <action type="shell_command">sed -i.bak 's/-lz -L. -lbam/-lbam -lz -L./' Makefile</action>
-                <action type="shell_command">make</action>
-                <action type="move_directory_files">
-                    <source_directory>.</source_directory>
-                    <destination_directory>$INSTALL_DIR/lib/samtools</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="SAMTOOLS_ROOT" action="set_to">$INSTALL_DIR/lib/samtools</environment_variable>
-                </action>
-
-                <!-- Somatic Sniper -->
-                <action type="shell_command">git clone --recursive git://github.com/genome/somatic-sniper.git</action>
-                <action type="move_directory_files">
-                    <source_directory>.</source_directory>
-                    <destination_directory>$INSTALL_DIR/lib</destination_directory>
-                </action>
-                <action type="make_directory">$INSTALL_DIR/build</action>
-                <action type="shell_command">cmake $INSTALL_DIR/lib/somatic-sniper</action>
-                <action type="move_directory_files">
-                    <source_directory>$INSTALL_DIR/build/bin</source_directory>
-                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                </action> 
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        	Somatic-sniper compiled version is unstable, for stable version use debian package system apt-get, this install requires cmake and zlib (for samtools)
-        </readme>
-    </package>
-    
-    
-</tool_dependency>