# HG changeset patch
# User fcaramia
# Date 1354681500 18000
# Node ID f521f05bc6f5c7d0e4e49cedcdf08a753b282dbe
# Parent  d63052c0d852962e092eb55a3d367961f32cb4a7
Uploaded

diff -r d63052c0d852 -r f521f05bc6f5 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Dec 02 23:10:12 2012 -0500
+++ b/tool_dependencies.xml	Tue Dec 04 23:25:00 2012 -0500
@@ -1,22 +1,25 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="bedtools" version="2.17.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action>
-                <action type="shell_command">tar -zxvf BEDTools.v2.17.0.tar.gz </action>
-                <action type="shell_command">cd BEDTools.v2.17.0</action>
-                <action type="shell_command">make clean</action>
-                <action type="shell_command">make all</action>
-                <action type="shell_command">cp bin/* $INSTALL_DIR/bin</action>
-                
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
+   <package name="bedtools" version="2.17.0">
+       <install version="1.0">
+           <actions>
+		<action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz">http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action>
+		<action type="shell_command">tar -zxvf bedtools-2.17.0.tar.gz </action>
+		<action type="shell_command">cd bedtools-2.17.0</action>
+		<action type="shell_command">make clean</action>
+		<action type="shell_command">make all</action>
+		<action type="move_directory_files">
+			<source_directory>bin</source_directory>
+			<destination_directory>$INSTALL_DIR/bin</destination_directory>
+		</action>
+		<action type="set_environment">
+		   <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+		</action>
+           </actions>
+       </install>
+       <readme>
 GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools
-        </readme>
-    </package>
+       </readme>
+   </package>
 </tool_dependency>
+