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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