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
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-- 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.gruening@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/