Kerry,

Greg's fix in 11800:a53f2f700699 has been applied to the stable branch as 11804:a9a0ac9c1afa, and the galaxy-dist repository has been updated to that changeset.

--Dave B.

On 12/18/2013 07:14 PM, Kerry Deutsch wrote:

No, we're pulling galaxy-dist.

Thanks for the quick reply, Kerry

On Wed, Dec 18, 2013 at 4:07 PM, Greg Von Kuster <greg@bx.psu.edu mailto:greg@bx.psu.edu> wrote:

Hello Kerry,

I've committed a fix for this in 11800:a53f2f700699 to the
galaxy-central branch.  Is that the branch you're pulling?

Thanks for reporting this.

Greg Von Kuster

On Dec 18, 2013, at 5:48 PM, Kerry Deutsch
<Kerry.Deutsch@systemsbiology.org
<mailto:Kerry.Deutsch@systemsbiology.org>> wrote:

 >
 > Hello -
 >
 > I pulled down the latest changes today (it was long overdue), and
am running into the following error when I run the tool migration:
 >
 > sh ./scripts/migrate_tools/0008_tools.sh install_dependencies
 > No handlers could be found for logger "galaxy.tools.data"
 > Repositories will be installed into configured tool_path location
  ../shed_tools
 > [localhost] local: rm -rf ./database/tmp/tmp-toolshed-mtdWuQjBx
 >
 > Skipping installation of tool dependency samtools version 0.1.18
since it is installed in
/users/galaxy/galaxy_deps/bin/samtools/0.1.18/devteam/package_samtools_0_1_18/171cd8bc208d
 >
 > Traceback (most recent call last):
 >  File "./scripts/migrate_tools/migrate_tools.py", line 21, in
<module>
 >    app = MigrateToolsApplication( sys.argv[ 1 ] )
 >  File
"/users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py",
line 83, in __init__
 >    install_dependencies=install_dependencies )
 >  File
"/users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
line 121, in __init__
 >    is_repository_dependency=is_repository_dependency )
 >  File
"/users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
line 509, in install_repository
 >    is_repository_dependency=is_repository_dependency )
 >  File
"/users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
line 351, in handle_repository_contents
 >    guid = self.get_guid( repository_clone_url,
relative_install_dir, tool_config )
 >  File
"/users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
line 259, in get_guid
 >    full_path = str( os.path.abspath( os.path.join( root, name ) ) )
 > UnboundLocalError: local variable 'name' referenced before assignment
 >
 >
 > Ideas?
 >
 > Thanks much!
 > Kerry
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