Hi, I'm having difficulties with the Tool Shed. I've got a freshly installed setup of galaxy-dist to run the community from and I'm trying to Upload files to a repository but getting an error when I do. My user requires the "NGS: QC and manipulation" section of tools as well as others and so I'm trying to import these into a local Tool Shed. I have therefore downloaded the tar.gz file from the public Galaxy Tool Shed, of the repository of the first tool listed within "NGS: QC and manipulation", the FASTQ Groomer, which is "sharplabtool" from http://toolshed.g2.bx.psu.edu/repository/view_repository?id=ecc93bc8f0382e9e&changeset_revision=c2a356708570 Every time I attempt to do this upload, I have the following Server Error reported: ### Module paste.exceptions.errormiddleware:143 in __call__
<http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=9ed9121ed2b0078e> 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=9ed9121ed2b0078e> environ, self.app) Module paste.wsgilib:539 in intercept_output <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=9ed9121ed2b0078e> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=9ed9121ed2b0078e> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=9ed9121ed2b0078e> 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=9ed9121ed2b0078e> body = method( trans, **kwargs ) Module galaxy.web.framework:94 in decorator <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=9ed9121ed2b0078e> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.community.controllers.upload:183 in upload <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=9ed9121ed2b0078e> set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str, **kwd ) Module galaxy.webapps.community.controllers.common:634 in set_repository_metadata_due_to_new_tip <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=9ed9121ed2b0078e> error_message, status = set_repository_metadata( trans, repository, content_alert_str=content_alert_str, **kwd ) Module galaxy.webapps.community.controllers.common:583 in set_repository_metadata <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=9ed9121ed2b0078e> persist=False ) Module galaxy.util.shed_util_common:711 in generate_metadata_for_changeset_revision <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=9ed9121ed2b0078e> invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_metadata_paths ) Module galaxy.util.shed_util_common:246 in check_tool_input_params <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=9ed9121ed2b0078e> if options.tool_data_table or options.missing_tool_data_table_name: AttributeError: 'str' object has no attribute 'tool_data_table' ###
Can anyone help me as to why this happens and how I fix it? Any alternative suggestions as to how I can clone repo's from one Tool Shed to another would also be appreciated. Many Thanks, Adam. --- Adam Carr Linux Support & Developmnent E adam.carr@nbi.ac.uk T +44 1603 450161 W jic.ac.uk ifr.ac.uk tgac.ac.uk tsl.ac.uk NBI Partnership Ltd Norwich Research Park Norwich NR4 7UH The NBI Partnership Ltd provides non-scientific services to the Institute of Food Research, the John Innes Centre, The Genome Analysis Centre and The Sainsbury Laboratory