Hi Bjoren, What revision are you seeing this in? I don't think this issues exists in Galaxy central's tip, but let me know.
Thanks! Greg On Jun 8, 2012, at 10:44 AM, Björn Grüning wrote: > Hi Greg, > > thanks! I can confirm that it is working now. I can upload new > datatypes. > What is not working is the update of such tools from the toolshed. > I get the following error. > > URL: > http://localhost/toolshed/repository/check_for_updates?galaxy_url=http://localhost/&name=molecule_datatypes&owner=admin&changeset_revision=2a638740087d&webapp=galaxy&no_reset=true > Module paste.exceptions.errormiddleware:143 in __call__ >>> app_iter = self.application(environ, start_response) > Module paste.debug.prints:98 in __call__ >>> environ, self.app) > Module paste.wsgilib:539 in intercept_output >>> app_iter = application(environ, replacement_start_response) > Module paste.recursive:80 in __call__ >>> return self.application(environ, start_response) > Module paste.httpexceptions:632 in __call__ >>> return self.application(environ, start_response) > Module galaxy.web.framework.base:160 in __call__ >>> body = method( trans, **kwargs ) > Module galaxy.webapps.community.controllers.repository:684 in > check_for_updates >>> url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() ) > UnboundLocalError: local variable 'latest_ctx' referenced before > assignment > > Removing and installing works fine. > If you need more information to track that bug done, let me know. > > Cheers, > Bjoern > > >> Hello Bjoern, >> >> This should be resolved in change set 7211:16a93eb6eaf6, which is available >> from our central repository. Thanks for reporting this, and please let me >> know if you encounter additional issues. >> >> Greg Von Kuster >> >> >> On May 26, 2012, at 10:51 AM, Björn Grüning wrote: >> >>> Hi, >>> >>> has anyone encountered that problem or has an idea how to solve it? >>> >>> Traceback (most recent call last): >>> File "/home/ctb/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in >>> app_factory >>> app = UniverseApplication( global_conf = global_conf, **kwargs ) >>> File "/home/ctb/galaxy-dist/lib/galaxy/app.py", line 64, in __init__ >>> self.installed_repository_manager.load_proprietary_datatypes() >>> File "/home/ctb/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/ctb/galaxy-dist/lib/galaxy/util/shed_util.py", line 1036, >>> in load_datatype_items >>> app.datatypes_registry.load_datatype_converters( app.toolbox, >>> installed_repository_dict=repository_dict, deactivate=deactivate ) >>> AttributeError: 'UniverseApplication' object has no attribute 'toolbox' >>> >>> All files are in one repository ... xml, the python-class und the >>> converters. I was able to successfully upload it to our test-toolshed >>> but after installing it (also successfully) galaxy is not able to start. >>> Also the converters are recognised as tools in the toolshed is that >>> intended? >>> >>> Thanks! >>> Bjoern >>> >>> ___________________________________________________________ >>> 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/ >> > > -- > Björn Grüning > Albert-Ludwigs-Universität Freiburg > Institute of Pharmaceutical Sciences > Pharmaceutical Bioinformatics > Hermann-Herder-Strasse 9 > D-79104 Freiburg i. Br. > > Tel.: +49 761 203-4872 > Fax.: +49 761 203-97769 > E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de > Web: http://www.pharmaceutical-bioinformatics.org/ > ___________________________________________________________ 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/
