# HG changeset patch
# User jmchilton
# Date 1377556103 14400
# Node ID 775c869b5ecdd5ba5c9ebdcf62bf45c71c6b53ce
# Parent  31ef98aa532debfbb054a95ba8239b58d17b4b30
Uploaded

diff -r 31ef98aa532d -r 775c869b5ecd tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Aug 26 18:12:33 2013 -0400
+++ b/tool_dependencies.xml	Mon Aug 26 18:28:23 2013 -0400
@@ -1,5 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
+  <!--
     <package name="tophat2" version="2.0.8b">
         <install version="1.0">
             <actions>
@@ -10,15 +11,17 @@
           Tophat2.
         </readme>
     </package>
+    -->
     <package name="tophat" version="1.3.3">
         <install version="1.0">
             <actions>
-              <action type="cloudbiolinux_install" cbl_url="https://github.com/chapmanb/cloudbiolinux/archive/master.zip" /> <!-- Grab package name and version from package statement. -->
+              <action type="cloudbiolinux_install" cbl_url="https://github.com/jmchilton/cloudbiolinux/archive/master.zip" /> <!-- Grab package name and version from package statement. -->
             </actions>
         </install>
         <readme>TopHat 1.3.3.
         </readme>
     </package>
+    <!--
     <package name="cufflinks2" version="2.1.1">
         <install version="1.0">
             <actions>
@@ -29,4 +32,5 @@
           Cufflinks2.
         </readme>
     </package>
+    -->
 </tool_dependency>
\ No newline at end of file