Hi Derrick,
The wiki page to which you refer describes the manual way that the Galaxy admin
can install tool dependencies (using a manual process). The tool shed
automatically does everything to install repositories, tools, tool
dependencies, datatypes, and other repository contents. If you
Thanks Greg,
Indeed, I tried to be smart and removed the entries from tool conf xml
before running the script. :)
About the missing dependencies, I still couldn't make it happy. I have
added:
$GALAXY_ROOT/tool_dependency_dir/bwa/0.5.9/env.sh
and add appropriate export PATH inside the env.sh,
Okay,
I found the button for installing the dependencies. The files are installed:
galaxy-dist/tool_dependency_dir/bwa/0.5.9/devteam/bwa_wrappers/ffa8aaa14f7c
Quite different from what the wiki states..
http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
Derrick
On Wed, Oct 10, 2012
Hi guys,
I have updated the galaxy to Oct 5 dist, and BWA has been reinstalled via
the migration script. However, I couldn't find any entry has been added
in migrated_tools_conf.xml (thus the BWA tools are not display in the tool
panel).
I check in the admin Installed tool shed repositories
Hi Derrick,
I am not able to reproduce this behavior, so it's difficult to tell what
problem may have occurred that resulted in the entries for the bwa tools to not
be added to you migrated_tools_conf.xml file. Choosing to install or not
install tool dependences makes no difference in whether
Hi Greg,
I did another test on a fresh installed galaxy Oct 5 release, I simply
cloned from the galaxy-dist, start the server once so everything's
populated, then here was how I ran the migration script and output:
pwbcad@gamma00:galaxy-dist$ sh ./scripts/migrate_tools/0005_tools.sh
No handlers
Can I actually just skip executing the migration script, and just install
BWA from the tool shed like I did for other shed tools?? Should be fine I
guess?
Derrick
On Tue, Oct 9, 2012 at 11:49 AM, Derrick Lin klin...@gmail.com wrote:
Hi Greg,
I did another test on a fresh installed galaxy Oct
