<?xml version="1.0"?>
<tool_dependency>
	
	<package name="cgatools17" version="1"> 
		<install version="1.0">
			<actions>
				<action type="download_by_url">http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz</action>
				<action type="shell_command"> chmod a+x bin/cgatools</action>
				<action type="move_file">
					<source>bin/cgatools</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 the cgatools binary. 
		</readme>
	</package>
	
	<package name="vcf_to_listVariants" version="1.0.0">
		<install version="1.0">
			<actions>
				<!--
				<action type="move_file">
					<source>$REPOSITORY_INSTALL_DIR/cgatools_v17/bin/vcf_to_listVariants.py</source>
					<destination>$INSTALL_DIR/bin/</destination>
				</action>
				-->
				
				<action type="shell_command">cp $REPOSITORY_INSTALL_DIR/tools/cgatools17/vcf_to_listVariants.py $INSTALL_DIR</action>
				<action type="chmod">
					<file mode="755">$INSTALL_DIR/vcf_to_listVariants.py</file>
				</action>
				
				<action type="set_environment">
					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR/cgatools_v17/bin</environment_variable>
					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR/cgatools_v17</environment_variable>
					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR/bin</environment_variable>
				</action>
			</actions>
		</install>
	</package>
	
</tool_dependency>