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.deut...@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/ ___________________________________________________________ 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/
