# HG changeset patch
# User stef
# Date 1402918986 14400
# Node ID b430d4b842336bd35a844f32eb835d0b662a6ad5
# Parent  2671b48cc122b9150e768549f55817e5b3450768
wget instead of download_by_url

diff -r 2671b48cc122 -r b430d4b84233 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jun 16 07:43:06 2014 -0400
@@ -0,0 +1,38 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	
+	<set_environment version="1.0">
+     	<environment_variable name="QDNASEQ_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+     </set_environment>
+
+	<package name="R" version="3.0.3">
+		<repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/" />
+	</package>
+	
+	<package name="bioc_qdnaseq" version="1.0.5">
+		<install version="1.0">
+			<actions>
+				<!--<action type="download_by_url">
+					http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz
+				</action>-->
+				<action type="shell_command">wget http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</action>
+				<action type="set_environment_for_install">
+					<repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/">
+						<package name="R" version="3.0.3" />
+					</repository>
+				</action>
+				<!-- <action type="shell_command">export R_LIBS=$INSTALL_DIR &amp;&amp; R CMD INSTALL QDNAseq_1.0.5.tar.gz</action> -->
+				<action type="shell_command">R CMD INSTALL QDNAseq_1.0.5.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.
+		</readme>
+	</package>
+		
+</tool_dependency>