--- a/tool_dependencies.xml	Mon Feb 17 09:49:16 2014 -0500
+++ b/tool_dependencies.xml	Thu Feb 20 08:57:09 2014 -0500
@@ -1,26 +1,11 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="R" version="2.11.0">
-        <repository changeset_revision="8d0a55bf7aaf" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="50f7e1e71271" name="package_r_3_0_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="bedtools" version="2.18.2">
-	<install version="1.0">
-		<actions>
-			<action type="download_by_url" target_filename="bedtools2-2.18.2.tar.gz" >https://github.com/arq5x/bedtools2/archive/v2.18.2.tar.gz</action>
-			<action type="shell_command">make</action>
-			<action type="move_file">
-				<source>bin/</source>	
-				<destination>$INSTALL_DIR/bin</destination>
-			</action>
-			<action type="set_environment">
-				<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-               		</action>
-            	</actions>
-        </install>
-        <readme>
-		Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
-     	</readme>
-   </package>
+	<repository changeset_revision="35905f2ae9f4" name="package_bedtools_2_18_2" owner="geert-vandeweyer" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
    <package name="samtools" version="0.1.18">
 	<repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>