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 <g...@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: > > http://lists.bx.psu.edu/ > > >
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