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.gruening@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: