Hello Sarah,

This is due to a known bug (not yet fixed in the distribution).  The bug causes 
the file named "datatypes_conf.xml" included in installed repositories to be 
deleted.  You'll need to go to the directory  on disk where your 
emboss_datatypes repository is installed ( make sure you are in the directory 
where the file named datatypes_conf.xml exists in the installed repository 
directory) and type the following command (this will undelete the file).

%hg revert datatypes_conf.xml


If you'd like to apply a fix to the code in your local instance, do the 
following.

You'll need to apply the fix to the file ~/lib/galaxy/util/shed_util.py.  The 
end of the method named alter_config_and_load_proprietary_datatypes() looks 
like the following (these lines should be about 601 - 607 in your version of 
the file, I believe).

    # Load proprietary datatypes
    app.datatypes_registry.load_datatypes( root_dir=app.config.root, 
config=proprietary_datatypes_config, deactivate=deactivate, override=override )
    try:
        os.unlink( proprietary_datatypes_config )
    except:
        pass
    return converter_path, display_path

You'll need to make this change (note the if statement that now contains the 
try block):

    # Load proprietary datatypes
    app.datatypes_registry.load_datatypes( root_dir=app.config.root, 
config=proprietary_datatypes_config, deactivate=deactivate, override=override )
    if datatype_files:
        try:
            os.unlink( proprietary_datatypes_config )
        except:
            pass
    return converter_path, display_path

Sorry for the inconvenience - I'll get this fix out as soon as I possibly can.  
Let me know if you bump into any problems with this.

Greg Von Kuster


On Feb 24, 2012, at 10:42 AM, Sarah Diehl wrote:

> Hi all,
> 
> I just updated our Galaxy from the latest dist to the latest central release. 
> When I had previously updatet to the dist release, the emboss datatypes were 
> installed as a shed tool. However when restarting the server after the update 
> the datatypes_conf.xml in the emboss shed directory got deleted. After some 
> back and forth I ended up with the following error, which I can't seem to 
> resolve.
> 
> galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-24 16:32:28,780 Loaded 
> reference to tool shed: Galaxy main tool shed
> galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-24 16:32:28,780 Loaded 
> reference to tool shed: Galaxy test tool shed
> Traceback (most recent call last):
>  File "/galaxy/galaxy_server/lib/galaxy/web/buildapp.py", line 82, in 
> app_factory
>    app = UniverseApplication( global_conf = global_conf, **kwargs )
>  File "/galaxy/galaxy_server/lib/galaxy/app.py", line 58, in __init__
>    self.installed_repository_manager.load_proprietary_datatypes()
>  File "/galaxy/galaxy_server/lib/galaxy/tool_shed/__init__.py", line 21, in 
> load_proprietary_datatypes
>    datatypes_config = metadata[ 'datatypes_config' ]
> KeyError: 'datatypes_config'
> 
> Any help would be greatly appreciated! Thanks!
> 
> Sarah
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