Sorry Greg, I hadn't spotted your other questions there. I'm fairly certain this must be a problem with the repository download I took as a .tar.gz from the main Galaxy Tool Shed: http://toolshed.g2.bx.psu.edu/repository/view_repository?id=ecc93bc8f0382e9e&changeset_revision=c2a356708570 I have tested this on a prior revision and the same error reoccurs. I'm installing this clean for each test, to walk you through my process... su - postgres psql postgres=# DROP DATABASE toolshed; postgres=# CREATE DATABASE toolshed OWNER galaxy TEMPLATE template0; postgres=# \q exit su - galaxy cd toolshed/ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist cd galaxy-dist/ hg pull -u cp ../../community_wsgi.ini . chmod a+x ./*run* ./run.sh --daemon start; tail -F paster.log ./run.sh --daemon stop ./run_community.sh --daemon start; tail -F community_webapp.log I access the Tool Shed and register my account, I access the Admin menu and create a category. I create a new repository and from there attempt to upload files to repository, selecting the .tar.gz previously downloaded from the link above. This is when I receive the error: Module paste.exceptions.errormiddleware:143 in __call__
<http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583> environ, self.app) Module paste.wsgilib:539 in intercept_output <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583> body = method( trans, **kwargs ) Module galaxy.web.framework:94 in decorator <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.community.controllers.upload:184 in upload <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583> set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str, **kwd ) Module galaxy.webapps.community.controllers.common:884 in set_repository_metadata_due_to_new_tip <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583> error_message, status = set_repository_metadata( trans, repository, content_alert_str=content_alert_str, **kwd ) Module galaxy.webapps.community.controllers.common:833 in set_repository_metadata <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583> updating_installed_repository=False ) Module galaxy.util.shed_util:706 in generate_metadata_for_changeset_revision <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583> invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_metadata_paths ) Module galaxy.util.shed_util:310 in check_tool_input_params <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583> if options.tool_data_table or options.missing_tool_data_table_name: AttributeError: 'str' object has no attribute 'tool_data_table'
From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: 05 December 2012 13:43 To: Adam Carr (NBI) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Main toolshed broken?? ok, I'll wait on the additional information I requested. On Dec 5, 2012, at 6:56 AM, Adam Carr (NBI) wrote: Hi Greg, Thank you for helping me out here. I'm running on the galaxy-dist branch, changeset 8285:f364d992270c. Many Thanks, Adam. From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: 05 December 2012 11:20 To: Adam Carr (NBI) Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Main toolshed broken?? Hi Adam, I cannot help with this new issue without more information from you. What version of Galaxy are you running?