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:
v
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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