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view tool_dependencies.xml @ 27:c6463da87893 draft

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author yhoogstrate
date Tue, 20 May 2014 05:27:02 -0400
parents 86f91bf4ab4c
children f55cd338fcdd
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<?xml version="1.0"?>
<tool_dependency>
	
	<package name="package_r3" version="3.0.1">
		<repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
	</package>
	
	<package name="package_biocLite_edgeR_limma" version="2.12">
		<install version="1.0"> 
			<actions>
				<action type="set_environment_for_install">
					<repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
						<package name="r3" version="3.0.1" />
					</repository>
				</action>
				<action type="make_directory">$INSTALL_DIR</action>
				<action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &gt; $INSTALL_DIR/runme.R</action>
				<action type="shell_command">echo "installme=c('edgeR','limma')" &gt;&gt; $INSTALL_DIR/runme.R</action>
				<action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
				<action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
				<action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" &gt;&gt; $INSTALL_DIR/runme.R</action>
				<action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>
				<action type="shell_command">export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
			</actions>
		</install>
		<readme>
			Installs the bioc packages edgeR &amp; Limma
	   </readme>
	</package>
	
</tool_dependency>