If I drop the following two tables, would those be reconstructed again correctly if I had the XML files in order?
tool_version_association
and
tool_version
Thanks
Thon
On Jul 11, 2012, at 12:29 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
On Jul 11, 2012, at 12:29 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
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
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