view tool_dependencies.xml @ 78:398963a4827a draft

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<?xml version="1.0"?>
<tool_dependency>
	
	<!-- the following repo does NOT work out of the box:
	<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>
	-->
	
	<!-- the following repo does NOT even install due to gfortran shared libs:
	<package name="R" version="3.1.0">
		<repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
	</package>
	-->
	
	<package name="R" version="3.0.3">
		<repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
	</package>
	
	<package name="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>
					-->
					<!-- the following repo does NOT even install due to gfortran shared libs:
					<repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
						<package name="R" version="3.1.0" />
					</repository>
					-->
					
					<repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
						<package name="R" version="3.0.3" />
					</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>
	
	<!-- instead of using "convert", make use of "gm convert" -->
	<package name="graphicsmagick" version="1.3.18">
		<repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
	</package>
</tool_dependency>