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
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