Galaxy on a server without internet connexion try to contact toolshed.g2.bx.psu.edu
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
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.Ghislain@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
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participants (2)
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Ghislain Fournous -
Greg Von Kuster