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.c...@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
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