Hi Derrick!

> I saw that printed message but I decided not to
> append install_dependencies flag to the command because we have had
> BWA binary in the galaxy running environment. 

> I don't think the use of install_dependencies is compulsory?

Sorry, im not sure if it is compulsory. But i would advise you do use
that. One idea of the toolshed is to log all version informations about
all dependencies, enabling reproducibility. Also the toolshed can create
environments for each tool, so that you can run different versions of
your tool. So it can be that the bwa-wrapper does not know about your
local install. But i haven’t looked at it. 

Regards,
Bjoern

> 
> Derrick
> 
> On Mon, Oct 8, 2012 at 5:14 PM, Björn Grüning
> <bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
>         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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>         
>         
> 
> 


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