# HG changeset patch
# User stef
# Date 1403081216 14400
# Node ID 5f8b99ae75efd6d1db1e1a6785b4ee86fa27b7b4
# Parent  5e5611bc7497aa176f639418183ee649ccecbdab
Uploaded

diff -r 5e5611bc7497 -r 5f8b99ae75ef tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jun 17 05:35:22 2014 -0400
+++ b/tool_dependencies.xml	Wed Jun 18 04:46:56 2014 -0400
@@ -1,59 +1,13 @@
 <?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="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/" />
-	</package>
-	
-	<package name="bioc_qdnaseq" version="1.0.5">
-		<install version="1.0">
-			<actions>
-				<action type="shell_command">echo "[DEBUG] INSTALL DIR: $INSTALL_DIR"</action>
-				<action type="shell_command">echo "[DEBUG] REPOS INSTALL DIR: $REPOSITORY_INSTALL_DIR"</action>
-				
-				<action type="shell_command">echo "[DEBUG] BEFORE:" &amp;&amp; pwd</action>
-				<action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>
-				<action type="shell_command">echo "[DEBUG] DIR LISTING ONE UP:" &amp;&amp; ls -l ../</action>
-				<!--
-				<action type="move_file">
-					<source>../QDNAseq.R</source>
-					<destination>./</destination>
-				</action>
-				-->
-				
-				<action type="shell_command">echo "[DEBUG] AFTER:" &amp;&amp; pwd</action>
-				<action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>
-
-				<action type="set_environment_for_install">
-					<repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/">
-						<package name="R" version="3.0.3" />
-					</repository>
-				</action>
-				<action type="set_environment">
-						<environment_variable action="prepend_to" name="R_LIBS">$INSTALL_DIR/bin</environment_variable>
-				</action>
-				<action type="shell_command">echo "[DEBUG] NOW ABOUT TO DOWNLOAD"</action>
-				
-				<action type="download_file">http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</action>
-				
-				<action type="shell_command">echo "[DEBUG] WORKING DIR:" &amp;&amp; pwd</action>
-				<action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>
-				
-				<action type="shell_command">echo "[DEBUG] NOW ABOUT TO INSTALL"</action>
-				<!--
-<action type="shell_command">export R_LIBS=$INSTALL_DIR &amp;&amp; R CMD INSTALL --> <!--build QDNAseq_1.0.5.tar.gz</action>
-				-->
-				<!--<action type="shell_command">R CMD INSTALL QDNAseq_1.0.5.tar.gz</action>-->
-			</actions>
-		</install>
-		
-		<readme>
-			Should install QDNAseq package from bioconductor.
-		</readme>
-	</package>
-		
-</tool_dependency> 
+    <!-- There is no R 3.1.0 package yet which is required due to bioconductor 2.14 package -->
+    <!-- As soon as it is available the dependencies will be set via "package_qdnaseq_1_0_5" -->
+    <!--
+    <package name="R_3_1_0" version="3.1.0">
+        <repository name="package_r_3_1_0" owner="iuc"/>
+    </package>
+    <package name="qdnaseq" version="1.0.5">
+        <repository name="package_qdnaseq_1_0_5" owner="stef"/>
+    </package>
+    -->
+</tool_dependency>