[galaxy-dev] The migrated BWA installed but missing dependencies

Hi guys, I have updated the galaxy to Oct 5 dist, and BWA has been reinstalled via the migration script. However, I couldn't find any entry has been added in migrated_tools_conf.xml (thus the BWA tools are not display in the tool panel). I check in the admin "Installed tool shed repositories" section and BWA repos status is "Installed, missing dependencies", is that why it didn't get added into the migrated_tools_conf.xml? I have had BWA 0.5.9-r16 in path, and been used by the old BWA wrapper without an issue before. How can I fix this dependencies issue for a Shed Tool? Should I add something like: <tool_dependency_dir>/bowtie/0.12.7/env.sh thanks, Derrick