Mercurial > repos > yhoogstrate > edger_with_design_matrix

changeset 24:86f91bf4ab4c draft

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Uploaded
author yhoogstrate
date Tue, 20 May 2014 05:26:25 -0400
parents fa476f8e1f9e
children 7cb518091b18
files tool_dependencies.xml
diffstat 1 files changed, 31 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue May 20 05:26:25 2014 -0400
@@ -0,0 +1,31 @@
+<?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>