Mercurial > repos > yhoogstrate > edger_with_design_matrix

view tool_dependencies.xml @ 61:415b1fabdd4a draft

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author yhoogstrate
date Tue, 30 Sep 2014 05:08:49 -0400
parents bcc237ae7050
children 829cabfc4707
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<?xml version="1.0"?>
<tool_dependency>
	
	<package name="package_r3_withx" version="3.0.1">
		<repository changeset_revision="abc274f22004" name="package_r3_withx" owner="joachim-jacob" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
	</package>
	
	<package name="package_biocLite_edgeR_limma" version="latest">
		<install version="1.0"> 
			<actions>
				<action type="set_environment_for_install">
					<!-- the following repo does NOT work out of the box:
					<repository changeset_revision="abc274f22004" name="package_r3_withx" owner="joachim-jacob" toolshed="http://testtoolshed.g2.bx.psu.edu/">
						<package name="package_r3_withx" version="3.0.1" />
					</repository>
					-->
					<repository changeset_revision="b6fe8ca3230d" name="package_r_3_0_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
						<package name="R_3_0_2" version="3.0.2" />
					</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 latest bioc packages edgeR &amp; Limma
	   </readme>
	</package>
	
</tool_dependency>