Hi Greg,
thanks for the help! However, the error still persists. I tried to play
around with lots of things, but nothing seems to change the error.
Sarah
On 02/24/2012 05:06 PM, Greg Von Kuster wrote:
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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