On Jul 11, 2012, at 3:38 PM, Anthonius deBoer wrote:

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...

This could pose problems unless you are sure that your code is in a functional state after you pull the latest revision from Galaxy central.

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....

The tools themselves are not "defined by the database", but metadata about the tools id stored in the database. For each repository you install from the tool shed, you will have 1 row in the tol_shed_repository table in your database. This table has a column named metadata that stores this information about the repository, including its contents (tools, datatypes, workflows, etc).

I have on occasions manually edited the XML file which I guess screws up the database...

Possibly. If you install a repository from the tool shed that includes a tool config, changing your local version of the tool config could pose problems if you get updates for your installed repository from the tool shed. If you don't do this, however, there should be no problem caused by changing your local version of the tool config.

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....

The way the tool shed components are architected do not result in this "syncing issues". You do not have to use the tool shed at all. Based on your statements that you like to change your versions of the tool configs and Galaxy code, you can protect your version of things by not running the tool migration scripts at all. Your Galaxy instance will still work as you expect.

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 <greg@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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