New subject: Galaxy on a server without internet connexion try to contact toolshed.g2.bx.psu.edu

4 Jul 2013

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_w...
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_c...
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&am...
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_pa...
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

    