Hi Thon,
What revision of Galaxy are you running? Have you made multiple attempts at
the migration? Are you running a postgres database? How many records do you
have in your tool_dependency table in your database, and what is the status of
each record? Have you made any changes to the Galaxy code base in your
environment? Any additional information that you can send will help track down
the problem in your environment.
Thanks!
Greg Von Kuster
On Jul 11, 2012, at 2:46 PM, Anthonius deBoer wrote:
> I'm getting this error when I try to run the tool migration:
>
> sh ./scripts/migrate_tools/0003_tools.sh install_dependencies
> No handlers could be found for logger "docutils"
> Repositories will be installed into configured tool_path location
> ../shed_tools
> Adding new row (or updating an existing row) for repository 'freebayes' in
> the tool_shed_repository table.
> Traceback (most recent call last):
> File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module>
> app = MigrateToolsApplication( sys.argv[ 1 ] )
> File
> "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/migrate/common.py", line
> 150, in __init__
> install_dependencies=install_dependencies )
> File
> "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/install_manager.py",
> line 37, in __init__
> self.install_repository( repository_elem, install_dependencies )
> File
> "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/install_manager.py",
> line 258, in install_repository
> install_dependencies=install_dependencies )
> File
> "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/install_manager.py",
> line 174, in handle_repository_contents
> tool_dependencies=tool_dependencies )
> File "/home/tdeboer/code/galaxy-copy/lib/galaxy/util/shed_util.py", line
> 1231, in handle_tool_dependencies
> tool_dependency = install_package( app, elem, tool_shed_repository,
> tool_dependencies=tool_dependencies )
> File
> "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/tool_dependencies/install_util.py",
> line 52, in install_package
> install_dir = get_tool_dependency_install_dir( app, tool_shed_repository,
> package_name, package_version )
> File
> "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/tool_dependencies/install_util.py",
> line 42, in get_tool_dependency_install_dir
> repository.installed_changeset_revision ) )
> File "/home/tdeboer/code/galaxy_env/lib/python2.6/posixpath.py", line 67,
> in join
> elif path == '' or path.endswith('/'):
> AttributeError: 'NoneType' object has no attribute 'endswith'
>
> Any ideas?
>
> Thanks
>
> Thon
> ___________________________________________________________
> 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/
___________________________________________________________
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/
