[galaxy-dev] Error resolving Emboss tool dependencies

I have migrated Emboss tool from dist to tool-shed using the migration script and later updated it's revision. The tool was installed along with it's dependencies, but it's failing to find them during job run. It's logging following 'Failed to resolve dependency on 'emboss', ignoring' warning message in the log file. It seems like build_dependency_shell_commands method in '/lib/galaxy/tools/__init__.py' is unable to get installed_tool_dependencies. I am not sure why this would fail and how to resolve it. I have tried resetting tool metadata several times, but that didn't help. Appreciate any help on resolving this error. I am using Galaxy release_2013.06.03 revision.

Thanks, Shantanu