My Galaxy version is the most recent, but I had cloned this from an earlier version and have made lots of changes over the months...
I'm a little confused by the fact that the tool_shed tools seem to be defined BOTH by the various XML files AND the database....
I have on occasions manually edited the XML file which I guess screws up the database...
it is bad practice to have two different places that can easily get out of sync I would think...Either stick with the XML paradigm OR move everything into a database...Doing both is bound to get out of sync....
I don't really want to dive into the database since I don't know the schema and not that good at SQL to begin with, but maybe a script that would sync stuff would be an idea...
Thanks
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
> ___________________________________________________________
> 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/
