Hi, I installed Galaxy on a server located on a secure Network without internet connexion following this instructions: http://wiki.galaxyproject.org/Admin/Config/Eggs
For an offline usage I changed the following parameters: Desable eggs check in run.sh FETCH_EGGS to 0 And the toolshed check option in universe_wsgi.ini enable_tool_shed_check = False On the first run Galaxy run, but when I tried to restart Galaxy try to contact toolshed.g2.bx.psu.edu : #--------------------------- The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_wrappers&owner=devteam&changeset_revision=0c7e4eadfb3c&from_install_manager=True raised the exception: <urlopen error [Errno -3] Temporary failure in name resolution> The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_color_wrappers&owner=devteam&changeset_revision=fd0914e451c5&from_install_manager=True raised the exception: <urlopen error [Errno -3] Temporary failure in name resolution> The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastz&owner=devteam&changeset_revision=0801f8207d30&from_install_manager=True raised the exception: <urlopen error [Errno -3] Temporary failure in name resolution> The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastz_paired_reads&owner=devteam&changeset_revision=96825cee5c25&from_install_manager=True raised the exception: <urlopen error [Errno -3] Temporary failure in name resolution> Traceback (most recent call last): File "/usr/local/Galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/usr/local/Galaxy/galaxy-dist/lib/galaxy/app.py", line 55, in __init__ verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/usr/local/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/check.py", line 55, in verify_tools tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number ) File "/usr/local/Galaxy/galaxy-dist/lib/tool_shed/util/common_util.py", line 67, in check_for_missing_tools return tool_shed_accessible, missing_tool_configs_dict UnboundLocalError: local variable 'missing_tool_configs_dict' referenced before assignment #--------------------------- I Fixed this problem by adding a enable_tool_shed_check check in lib/galaxy/app.py I'm new in the Galaxy World, so perhaps that is not an optimal way to fix this problem. diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -51,8 +51,9 @@ from galaxy.model.migrate.check import create_or_verify_database create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) # Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed. - from tool_shed.galaxy_install.migrate.check import verify_tools - verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) + if self.config.get_bool( 'enable_tool_shed_check', False ): + from tool_shed.galaxy_install.migrate.check import verify_tools + verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) # Object store manager self.object_store = build_object_store_from_config(self.config) # Setup the database engine and ORM Regards, Ghislain ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
