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__
>>  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.web.framework:94 in decorator
>>  return func( self, trans, *args, **kwargs )
Module galaxy.webapps.community.controllers.upload:183 in upload
>>  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
>>  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
>>  persist=False )
Module galaxy.util.shed_util_common:711 in generate_metadata_for_changeset_revision
>>  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
>>  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