# HG changeset patch
# User jmchilton
# Date 1377552538 14400
# Node ID 197957f90a1706269b18700fce6bf3a4fc61512a
# Parent  a0d2334e0e3c29f9b59ab2061535a809253747a4
Uploaded

diff -r a0d2334e0e3c -r 197957f90a17 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Aug 06 23:37:08 2013 -0400
+++ b/tool_dependencies.xml	Mon Aug 26 17:28:58 2013 -0400
@@ -3,17 +3,17 @@
     <package name="tophat2" version="2.0.8b">
         <install version="1.0">
             <actions>
-              <action type="cloudbiolinux_install" cbl_revision="4bd005355991a5c8b855ea790ae75e8178ede8c1" tool_name="tophat2" tool_version="2.0.8b" />
+              <action type="cloudbiolinux_install" cbl_revision="master" tool_name="tophat2" tool_version="2.0.8b" />
             </actions>
         </install>
         <readme>
-          Tophat2
+          Tophat2.
         </readme>
     </package>
     <package name="tophat" version="1.3.3">
         <install version="1.0">
             <actions>
-              <action type="cloudbiolinux_install" /> <!-- Grab package name and version from package statement. -->
+              <action type="cloudbiolinux_install" cbl_url="https://github.com/chapmanb/cloudbiolinux/archive/ef0106dde6b8ba43d37eb72733e10a8565efcb9e.zip" /> <!-- Grab package name and version from package statement. -->
             </actions>
         </install>
         <readme>TopHat 1.3.3.
@@ -22,7 +22,7 @@
     <package name="cufflinks2" version="2.1.1">
         <install version="1.0">
             <actions>
-              <action type="cloudbiolinux_install" cbl_url="https://github.com/jmchilton/cloudbiolinux.git" tool_name="cufflinks" tool_version="2.1.1" />
+              <action type="cloudbiolinux_install" cbl_url="https://github.com/chapmanb/cloudbiolinux/archive/ef0106dde6b8ba43d37eb72733e10a8565efcb9e.zip" tool_name="cufflinks" tool_version="2.1.1" />
             </actions>
         </install>
         <readme>