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)