view tool_dependencies.xml @ 9:031f77d360ea draft

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<?xml version="1.0"?>
<tool_dependency>

		<package name="cmake" version="3.1.0">
			<repository changeset_revision="782e014e71f9" name="package_cmake_3_1_0" owner="malbuquerque" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
		</package>

		<package name="samtools" version="0.1.18">
			<repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
		</package>
	
		<package name="bamtools" version="2.3.0">
			<install version="1.0">
				<actions>
		
					<action type="shell_command">pwd &gt; ~/whereami-2</action>
		
					<action type="set_environment_for_install">
						<repository changeset_revision="782e014e71f9" name="package_cmake_3_1_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu">
							<package name="cmake" version="3.1.0" />
						</repository>
					</action>

					<action type="shell_command">pwd &gt; ~/whereami-1</action>

					<action type="set_environment_for_install">
						<repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu">
							<package name="samtools" version="0.1.18" />
						</repository>
					</action>
					
					<action type="shell_command">pwd &gt; ~/whereami0</action>	
					<action type="download_by_url">https://github.com/pezmaster31/bamtools/archive/v2.3.0.tar.gz</action>
					<action type="shell_command">pwd &gt; ~/whereami</action>
					<action type="shell_command">mkdir build</action>
					<action type="shell_command">pwd &gt; ~/whereami2</action>
					<action type="change_directory">build</action>
					<action type="shell_command">pwd &gt; ~/whereami3</action>
					<action type="shell_command">cmake ..</action>
					<action type="shell_command">pwd &gt; ~/whereami4</action>
					<action type="shell_command">make</action>
					<action type="shell_command">pwd &gt; ~/whereami5</action>
					<action type="change_directory">..</action>
					<action type="shell_command">pwd &gt; ~/whereami6</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="BAMTOOLS_ROOT">$INSTALL_DIR</environment_variable>
						<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
					</action>

				</actions>	
			</install>
		</package>

	</tool_dependency>