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.

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