Dear all,

I'm trying to migrate our local Galaxy server from a standalone server running 
on CentOS 5 to a setup that runs Galaxy in a Docker container 
(bgruening/galaxy-stable). Due to Docker and the setup of the container, almost 
all data, tools, configs etc. have to move to a different place. Since our old 
server is pretty cluttered up anyway, I would like to move just user data 
(logins, histories, datasets ...), but none of the tool installations, tool 
data or configs.

My plan was to start with a fresh and clean new Galaxy installation, transfer 
the datasets and the database and then reinstall all tools through the toolshed 
(of course there are many more small odds and ends that need fixing).

The problem is that after transfering the database, I always get an error when 
going to "Manage installed tool shed repositories" (see end of the mail). I 
tried just overwriting the pg_data directory (PostgreSQL versions are 
identical) and also exporting to sql (pg_dump) and importing in the new DB. 
Both times I made sure to run manage_db.sh upgrade afterwards. The error stays 
the same.

I can't make much sense of the error message, my only guess is that it looks 
for something that's not there. However, I really don't want to transfer the 
tool directories and tool configurations, because that will get messy and 
difficult, since many paths need to be adjusted. There's a high chance for 
error and this way I also carry over the clutter.

So is there a way to remove all tool installation information from the 
database, before I transfer it? Can this even be disentangled from the 
histories and datasets? Any help or other ideas on how to do this migration are 
highly appreciated!

Thanks,
Sarah



10.1.5.190 - - [16/Oct/2014:09:54:35 +0000] "GET 
/admin_toolshed/browse_repositories HTTP/1.1" 500 - 
"http://deep2:8080/admin/index"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; 
rv:32.0) Gecko/20100101 Firefox/32.0"
Error - <type 'exceptions.UnicodeDecodeError'>: 'ascii' codec can't decode byte 
0xe2 in position 393: ordinal not in range(128)
URL: http://deep2:8080/admin_toolshed/browse_repositories
File 'lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File '/galaxy-central/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 
in __call__
  return self.application(environ, start_response)
File '/galaxy-central/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', 
line 633 in __call__
  return self.application(environ, start_response)
File 'lib/galaxy/web/framework/base.py', line 132 in __call__
  return self.handle_request( environ, start_response )
File 'lib/galaxy/web/framework/base.py', line 190 in handle_request
  body = method( trans, **kwargs )
File 'lib/galaxy/web/framework/decorators.py', line 87 in decorator
  return func( self, trans, *args, **kwargs )
File 'lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 167 in 
browse_repositories
  return self.installed_repository_grid( trans, **kwd )
File 'lib/galaxy/web/framework/helpers/grids.py', line 306 in __call__
  kwargs=kwargs )
File 'lib/galaxy/web/framework/webapp.py', line 771 in fill_template
  return self.fill_template_mako( filename, **kwargs )
File 'lib/galaxy/web/framework/webapp.py', line 786 in fill_template_mako
  return template.render( **data )
File '/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in 
render
  return runtime._render(self, self.callable_, args, data)
File '/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in 
_render
  **_kwargs_for_callable(callable_, data))
File '/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in 
_render_context
  _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File '/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in 
_exec_template
  callable_(context, *args, **kwargs)
File '/galaxy-central/database/compiled_templates/base.mako.py', line 66 in 
render_body
  __M_writer(unicode(next.body()))
File '/galaxy-central/database/compiled_templates/grid_base.mako.py', line 91 
in render_body
  __M_writer(unicode(self.load()))
File '/galaxy-central/database/compiled_templates/grid_base.mako.py', line 120 
in render_load
  __M_writer(unicode( h.dumps( self.get_grid_config( embedded=embedded, 
insert=insert ) ) ))
File '/galaxy-central/database/compiled_templates/grid_base.mako.py', line 303 
in render_get_grid_config
  value = column.get_value( trans, grid, item )
File 'lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py', line 106 in 
get_value
  return suc.get_tool_shed_repository_status_label( trans.app, 
tool_shed_repository )
File 'lib/tool_shed/util/shed_util_common.py', line 829 in 
get_tool_shed_repository_status_label
  elif tool_shed_repository.tool_dependencies_being_installed:
File 'lib/galaxy/model/tool_shed_install/__init__.py', line 408 in 
tool_dependencies_being_installed
  for tool_dependency in self.tool_dependencies:
File 
'/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py',
 line 168 in __get__
File 
'/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py',
 line 453 in get
File 
'/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py',
 line 508 in _load_for_state
File 
'/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py',
 line 574 in _emit_lazyload
File 
'/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py',
 line 2115 in all
File 
'/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py',
 line 2341 in instances
File 
'/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
 line 3204 in fetchall
File 
'/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
 line 3171 in _fetchall_impl
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 393: 
ordinal not in range(128)
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