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> 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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