# HG changeset patch
# User bgruening
# Date 1420320203 18000
# Node ID 190a747ddaa8402014a12a30af7900a0e1e4a796
# Parent  effb7b4e45edb2cba5abac0b7fd6d8b904692864
Uploaded

diff -r effb7b4e45ed -r 190a747ddaa8 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Dec 05 13:31:24 2014 -0500
+++ b/tool_dependencies.xml	Sat Jan 03 16:23:23 2015 -0500
@@ -1,20 +1,22 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="weka" version="3.6.11">
+    <package name="bedtools" version="2.22">
         <install version="1.0">
-            <actions> 
-                <action type="download_by_url">http://sourceforge.net/projects/weka/files/weka-3-6/3.6.11/weka-3-6-11.zip</action>
-                <action type="move_file">
-                    <source>weka-3-6-11/weka.jar</source>
-                    <destination>$INSTALL_DIR</destination>
+            <actions>
+                <action type="download_by_url">https://github.com/arq5x/bedtools2/releases/download/v2.22.1/bedtools-2.22.1.tar.gz</action>
+                <action type="shell_command">make</action>
+                <action type="move_directory_files">
+                    <source_directory>bin</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
                 </action>
                 <action type="set_environment">
-                    <environment_variable name="WEKA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                 </action>
             </actions>
         </install>
-        <readme>
-            Weka requires a JAVA (1.5+) runtime evironment.
-        </readme>
+        <readme>BEDTools is a collection of utilities for comparing, summarizing, and intersecting genomic features in BED, GTF/GFF, VCF and BAM formats.</readme>
     </package>
 </tool_dependency>
+
+
+