view tool_dependencies.xml @ 32:2b6a44353622

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<?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>