Hi, Greg, Thank you for your information. It helped me figured out the problem. I had made some changes to registry.py before the update, but the update process didn't merge the changes in the new version. I included the changes in the new version to registry.py and the problem is gone :) Best, Luobin On Fri, Jun 1, 2012 at 10:19 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:

Hello Luobin,

This is a strange error, and one that I cannot reproduce. The app.datatypes_registry.load_datatypes method signature looks like the following, so I'm not sure how your environment is producing this behavior.

def load_datatypes( self, root_dir=None, config=None, deactivate=False, override=True ):

What is the result of typing the following in your Galaxy install directory?

hg heads

What about the following:

hg status

And then finally:

hg diff

Thanks,

Greg Von Kuster

On Jun 1, 2012, at 12:06 PM, Luobin Yang wrote:

Hi,

After I update galaxy-dist to the latest version, I got the following error message when I run run.sh command:

galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-01 09:57:15,503 Loaded reference to tool shed: Galaxy test tool shed Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 64, in __init__ self.installed_repository_manager.load_proprietary_datatypes() File "/home/galaxy/galaxy-dist/lib/galaxy/tool_shed/__init__.py", line 26, in load_proprietary_datatypes load_datatype_items( self.app, tool_shed_repository, relative_install_dir ) File "/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py", line 1024, in load_datatype_items converter_path, display_path = alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_install_dir, deactivate=deactivate ) File "/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py", line 236, in alter_config_and_load_prorietary_datatypes app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=proprietary_datatypes_config, deactivate=deactivate, override=override ) TypeError: load_datatypes() got an unexpected keyword argument 'override' ___________________________________________________________ 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:

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