Mercurial > repos > morinlab > package_bamtools_2_3_0

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planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/packages/package_bamtools_2_3_0 commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
author morinlab
date Tue, 11 Oct 2016 13:34:22 -0400
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<?xml version="1.0"?>
<tool_dependency>
	<package name="cmake" version="3.1.0">
		<repository changeset_revision="e9baec7e0438" name="package_cmake_3_1_0" owner="morinlab" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
	</package>
	<package name="samtools" version="0.1.18">
		<repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
	</package>
	<package name="bamtools" version="2.3.0">
		<install version="1.0">
			<actions>		
				<action type="download_by_url">https://github.com/pezmaster31/bamtools/archive/v2.3.0.tar.gz</action>
		
				<action type="set_environment_for_install">
					<repository changeset_revision="e9baec7e0438" name="package_cmake_3_1_0" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu">
						<package name="cmake" version="3.1.0" />
					</repository>
				</action>

				<action type="set_environment_for_install">
					<repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu">
						<package name="samtools" version="0.1.18" />
					</repository>
				</action>		
	
				<action type="shell_command">mkdir build</action>
				<action type="change_directory">build</action>
				<action type="shell_command">cmake ..</action>
				<action type="shell_command">make</action>
				<action type="change_directory">..</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>