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view tool_dependencies.xml @ 33:24e081b3a421 draft

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author malbuquerque
date Tue, 20 Jan 2015 19:17:38 -0500
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<?xml version="1.0"?>
<tool_dependency>
		
		<package name="boost" version="1.53.0">
			<repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
		</package>

		<package name="bamtools" version="2.3.0">
			<repository changeset_revision="ad46b5210186" name="package_bamtools_2_3_0" owner="malbuquerque" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
		</package>

		<package name="seqtk" version="1.0.0">
			<repository changeset_revision="35f0f4568ded" name="package_seqtk_1_0_0" owner="malbuquerque" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
		</package>
			
		<package name="delly" version="0.6.1">
			<install version="1.0">
				<actions>
					<action type="shell_command">ls</action>
					<action type="set_environment_for_install">
						<repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
							<package name="boost" version="1.53.0" />
						</repository>
					</action>
					<action type="shell_command">ls</action>
					<action type="set_environment_for_install">
						<repository changeset_revision="ad46b5210186" name="package_bamtools_2_3_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu">
							<package name="bamtools" version="2.3.0" />
						</repository>
					</action>
					<action type="shell_command">ls</action>
					<action type="set_environment_for_install">
						<repository changeset_revision="35f0f4568ded" name="package_seqtk_1_0_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu">
							<package name="seqtk" version="1.0.0" />
						</repository>
					</action>
					<action type="shell_command">ls</action>
					<action type="download_by_url">https://github.com/tobiasrausch/delly/archive/v0.6.1.tar.gz</action>
					<action type="shell_command">make -f $REPOSITORY_INSTALL_DIR/Makefile all BOOST_ROOT=$BOOST_ROOT_DIR/ BAMTOOLS_ROOT=$BAMTOOLS_ROOT/ SEQTK_ROOT=$SEQTK_ROOT/</action>
					<action type="move_directory_files">
						<source_directory>.</source_directory>
						<destination_directory>$INSTALL_DIR</destination_directory>
					</action>	
					<action type="set_environment">
						<environment_variable action="set_to" name="DELLY_DIR">$INSTALL_DIR</environment_variable>
					</action>
				</actions>
			</install>
		</package>

	</tool_dependency>