Mercurial > repos > stef > qdnaseq

changeset 0:e81046cbc191 draft

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Uploaded
author stef
date Fri, 13 Jun 2014 09:41:06 -0400
parents
children 75d96e0555d1
files tool_dependencies.xml
diffstat 1 files changed, 36 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Jun 13 09:41:06 2014 -0400
@@ -0,0 +1,36 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	
+	<set_environment version="1.0">
+     	<environment_variable name="QDNASEQ_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+     </set_environment>
+
+	<package name="R" version="3.0.3">
+		<repository changeset_revision="933ba62d2f11" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" />
+	</package>
+	
+	<package name="bioc_qdnaseq" version="1.0.4">
+		<install version="1.0">
+			<actions>
+				<action type="download_by_url">
+					http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.4.tar.gz
+				</action>
+				<action type="set_environment_for_install">
+					<repository changeset_revision="933ba62d2f11" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/">
+						<package name="R" version="3.0.3" />
+					</repository>
+				</action>
+				<action type="shell_command">export R_LIBS=$INSTALL_DIR &amp;&amp; R CMD INSTALL QDNAseq_1.0.4.tar.gz</action>
+				
+				<action type="set_environment">
+						<environment_variable action="prepend_to" name="R_LIBS">$INSTALL_DIR/bin</environment_variable>
+				</action>
+			</actions>
+		</install>
+		
+		<readme>
+			Should install QDNAseq package from bioconductor. Requires R galaxy package (3.0.3) to be installed.
+		</readme>
+	</package>
+		
+</tool_dependency>