# HG changeset patch
# User yhoogstrate
# Date 1391764299 18000
# Node ID dc091c635cf0fcf2cc751368f03a1d7cb6d996e3
# Parent  51fa0e2620f79be2c6a51e50beab71282cb8ab23
Uploaded

diff -r 51fa0e2620f7 -r dc091c635cf0 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Feb 07 04:11:39 2014 -0500
@@ -0,0 +1,39 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="samtools-mpileup-parallel" version="1.0.19">
+		<install version="1.0">
+			<actions>
+				<action type="shell_command">svn checkout https://github.com/mydatascience/parallel-mpileup/trunk samtools-mpileup-parallel &amp;&amp; cd samtools-mpileup-parallel &amp;&amp; cd $(ls |grep samtools-) &amp;&amp; make &amp;&amp; cp samtools ../samtools-mpileup-parallel</action>
+				<action type="move_file">
+					<source>samtools-mpileup-parallel</source>
+					<destination>$INSTALL_DIR/bin</destination>
+				</action>
+				<action type="set_environment">
+					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+				</action>
+			</actions>
+		</install>
+		<readme>
+			Downloads and installs a modified version of samtools, able to paralellize the mpileup function.
+		</readme>
+	</package>
+	<package name="VarScan" version="2.3.6">
+		<install version="1.0">
+			<actions>
+				<action type="shell_command">wget http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar --output-file="VarScan.v2.3.6.jar"</action>
+				<action type="move_file">
+					<source>../VarScan.v2.3.6.jar</source>
+					<destination>$INSTALL_DIR/bin</destination>
+				</action>
+				<action type="set_environment">
+					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+				</action>
+			</actions>
+		</install>
+		<readme>
+			Downloads VarScan2.
+		</readme>
+	</package>
+</tool_dependency>