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 > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/

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