Mercurial > repos > eganrol > rnaseqdataannotation

diff RNAseqDataAnnotation/tool_dependencies.xml @ 18:d1a60d1848d9 draft

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author eganrol
date Thu, 20 Nov 2014 03:51:36 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RNAseqDataAnnotation/tool_dependencies.xml	Thu Nov 20 03:51:36 2014 -0500
@@ -0,0 +1,26 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R_3_0_2" version="3.0.2">
+		<repository changeset_revision="b6fe8ca3230d" name="package_r_3_0_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="DESeq2biomaRt" version="1.0">
+		<install version="1.0">
+			<actions>
+                <action type="set_environment_for_install">
+					<repository changeset_revision="b6fe8ca3230d" name="package_r_3_0_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+						<package name="R_3_0_2" version="3.0.2" />
+					</repository> 
+				</action>
+                <action type="shell_command">R CMD BATCH source("http://bioconductor.org/biocLite.R")</action>
+                <action type="shell_command">R CMD BATCH biocLite()</action>
+                <action type="shell_command">R CMD BATCH biocLite("DESeq2")</action>
+                <action type="shell_command">R CMD BATCH biocLite("biomaRt")</action>
+                <action type="shell_command">R CMD BATCH install.packages("plyr")</action>
+				<!--<action type="shell_command">echo "export PATH=$PATH" > $INSTALL_DIR/env.sh </action>-->
+				<!--<action type="shell_command">chmod 755 $INSTALL_DIR/env.sh </action>-->
+			</actions> 
+       </install> 
+     <readme>
+     </readme> 
+   </package> 
+</tool_dependency>