Mercurial > repos > eganrol > rnaseqdataannotation

diff RNAseqDataAnnotation/tool_dependencies.xml @ 0:de3907c85546 draft

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author eganrol
date Wed, 19 Nov 2014 11:52:45 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RNAseqDataAnnotation/tool_dependencies.xml	Wed Nov 19 11:52:45 2014 -0500
@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.1.0">
+    <repository changeset_revision="0:a6cc7706ea14" name="package_r_3_1_0" 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="0:a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+						<package name="R" version="3.1.0" />
+					</repository>
+                </action>
+                <action type="shell_command">R CMD BATCH packages.R</action>
+                <action type="shell_command">echo "export PATH=$PATH" &gt; $INSTALL_DIR/env.sh </action>
+			    <action type="shell_command">chmod 755 $INSTALL_DIR/env.sh </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+</tool_dependency>