--- a/tool_dependencies.xml	Mon Sep 09 06:11:47 2013 -0400
+++ b/tool_dependencies.xml	Fri Jan 31 05:44:03 2014 -0500
@@ -1,5 +1,8 @@
 <?xml version="1.0"?>
 <tool_dependency>
+  <package name="bowtie2" version="2.1.0">
+    <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+  </package>
   <package name="edge-pro" version="1.3.1">
     <install version="1.0">
       <actions>
@@ -14,14 +17,15 @@
           <destination>$INSTALL_DIR/bin</destination>
         </action>
         <action type="set_environment">
-          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
         </action>
       </actions>
     </install>
     <readme>
 Dependencies of EDGE-pro which needs to be installed separately:
-- bowtie2 ( http://bowtie-bio.sourceforge.net/bowtie2/ ), in particular bowtie2, bowtie2-align and bowtie2-build need to be in the $PATH . These are usually already installed for Galaxy;
-- Switch Perl core module ( http://search.cpan.org/~rgarcia/Switch/Switch.pm ).
+- Switch Perl module ( http://search.cpan.org/~rgarcia/Switch/Switch.pm ).
+
+Configuration: Previously (until Release 0), the EDGE_PRO_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of threads to use (--num-threads). This is not used anymore and may be removed.
     </readme>
   </package>
 </tool_dependency>