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 could be found for logger "galaxy.tools.data"
RuntimeWarning: __builtin__.file size changed, may indicate binary
from csamtools import *
Repositories will be installed into configured tool_path location
Adding new row (or updating an existing row) for repository 'bwa_wrappers'
in the tool_shed_repository table.
The installation process is finished. You should now remove entries for
the installed tools from your file named
./tool_conf.xml and start your Galaxy server.
I then checked the migrated_tools_conf.xml but no entries for BWA still.
Note that I haven't run the previous migration scripts because I don't need
those tools. Will that be the issue?
On Tue, Oct 9, 2012 at 2:17 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> 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 the repository
> is installed and the tools are properly configured in the
> migrated_tools_conf.xml file and subsequently loaded into the Galaxy tool
> Can you try manually adding the following sections to your
> migrated_tools_conf.xml file and see if that solves your problem (of
> course, you can change the section id and name attributes if you want or
> eliminate the section altogether).
> <section id="solexa_tools" name="NGS: Mapping" version="">
> <tool file="../shed_tools/
> <tool file="../shed_tools/
> Greg Von Kuster
> On Oct 8, 2012, at 1:55 AM, Derrick LIN wrote:
> 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
> 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:
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