view tool_dependencies.xml @ 4:c2d97d59e527 draft

Uploaded

<?xml version="1.0"?>
<tool_dependency>
	
	<set_environment version="1.0">
     	<environment_variable name="QDNASEQ_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>

	<package name="R" version="3.0.3">
		<repository changeset_revision="933ba62d2f11" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/" />
	</package>
	
	<package name="bioc_qdnaseq" version="1.0.4">
		<install version="1.0">
			<actions>
				<action type="download_by_url">
					http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.4.tar.gz
				</action>
				<action type="set_environment_for_install">
					<repository changeset_revision="933ba62d2f11" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/">
						<package name="R" version="3.0.3" />
					</repository>
				</action>
				<action type="shell_command">export R_LIBS=$INSTALL_DIR &amp;&amp; R CMD INSTALL QDNAseq_1.0.4.tar.gz</action>
				
				<action type="set_environment">
						<environment_variable action="prepend_to" name="R_LIBS">$INSTALL_DIR/bin</environment_variable>
				</action>
			</actions>
		</install>
		
		<readme>
			Should install QDNAseq package from bioconductor. Requires R galaxy package (3.0.3) to be installed.
		</readme>
	</package>
		
</tool_dependency>