I would not advise doing this. Based on your environment, I recommend that you
do not attempt to install tools from the tool shed as doing so may pose
problems for the same tools that you have altered in your environment and that
you do not want to get "out of sync".
On Jul 11, 2012, at 4:09 PM, Anthonius deBoer wrote:
> 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:
>
>> 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/
