Hi Bjorn, 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? 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 > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > > > http://lists.bx.psu.edu/ > > >
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