# HG changeset patch
# User nilesh
# Date 1373308163 14400
# Node ID f88d3f39837c35827905c4fddd5c316a48bb7a6b
# Parent  0f0d22ae5a9262117cbfb985e7e375f1bd26e132
Deleted selected files

diff -r 0f0d22ae5a92 -r f88d3f39837c tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jul 08 13:50:26 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 -D Samtools_INCLUDE_DIR:PATH=$INSTALL_DIR/lib/samtools $INSTALL_DIR/lib/somatic-sniper</action>
-                <action type="move_directory_files">
-                    <source_directory>$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>