Hi Derrick,

i think during the migration something like that was printed on your
screen:

---------
The tool dependencies listed above will be installed along with the
repositories if you add the 'install_dependencies' option to the above
command like this:

vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
sh ./scripts/migrate_tools/0005_tools.sh install_dependencies
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Tool dependencies can be installed after the repositories have been
installed as well.
---------

I think you should run that command by yourself to get BWA working
again.

Kind regards,
Bjoern

> 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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