Hello Ghislain, Thanks very much for repostring this issue. I have committed a fix in changeset 10205:2accb50ef103.
Greg Von Kuster On Jul 4, 2013, at 7:21 AM, Ghislain Fournous <fournous.ghisl...@rr-research.no> wrote: > 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/ ___________________________________________________________ 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/
