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
I don't think the use of install_dependencies is compulsory?
On Mon, Oct 8, 2012 at 5:14 PM, Björn Grüning <
> Hi Derrick,
> i think during the migration something like that was printed on your
> 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:
> 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
> Kind regards,
> > 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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