view package/tool_dependencies.xml @ 3:b833f6538a4c draft

Uploaded

<?xml version="1.0"?>
<tool_dependency>
		
		<package name="boost" version="1.53">
			<repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" 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" 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" toolshed="https://toolshed.g2.bx.psu.edu" />
		</package>
			
		<package name="delly" version="0.6.1">
			<install version="1.0">
				<actions>
					<action type="download_by_url">https://github.com/tobiasrausch/delly/archive/v0.6.1.tar.gz</action>
					<action type="shell_command">git clone https://github.com/morinlab/galaxy_tools.git</action>
					<action type="move_directory_files">
						<source_directory>./galaxy_tools/delly/Makefile</source_directory>
						<destination_directory>.</destination_directory>
					</action>
					<action type="shell_command">make all BOOST_ROOT=\$BOOST_ROOT 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>