Hi, We've just installed the latest galaxy-dist: hg clone https://bitbucket.org/galaxy/galaxy-dist/ cd galaxy-dist hg -v update stable The server runs: CentOS release 6.5, python 2.6.8, and mysql-5.1.71-1.el6.x86_64 "sh run.sh" has failed: ...... migrate.versioning.repository DEBUG 2013-12-10 09:35:51,145 Repository lib/galaxy/model/migrate loaded successfully migrate.versioning.repository DEBUG 2013-12-10 09:35:51,145 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_version', 'repository_id': 'Galaxy'}} galaxy.model.migrate.check DEBUG 2013-12-10 09:35:51,152 MySQL_python egg successfully loaded for mysql dialect galaxy.model.migrate.check INFO 2013-12-10 09:35:51,309 No database, initializing Traceback (most recent call last): File "/wwwdata/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/wwwdata/galaxy/lib/galaxy/app.py", line 54, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) File "/wwwdata/galaxy/lib/galaxy/model/migrate/check.py", line 64, in create_or_verify_database db_schema = schema.ControlledSchema( engine, migrate_repository ) File "/wwwdata/galaxy/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/schema.py", line 32, in __init__ self.load() File "/wwwdata/galaxy/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/schema.py", line 44, in load self.table = Table(tname, self.meta, autoload=True) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py", line 318, in __new__ table._init(name, metadata, *args, **kw) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py", line 381, in _init self._autoload(metadata, autoload_with, include_columns) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py", line 408, in _autoload self, include_columns, exclude_columns File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2425, in run_callable return conn.run_callable(callable_, *args, **kwargs) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1968, in run_callable return callable_(self, *args, **kwargs) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 260, in reflecttable return insp.reflecttable(table, include_columns, exclude_columns) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py", line 350, in reflecttable tbl_opts = self.get_table_options(table_name, schema, **table.kwargs) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py", line 178, in get_table_options **kw) File "<string>", line 1, in <lambda> File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py", line 47, in cache ret = fn(self, con, *args, **kw) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 2064, in get_table_options parsed_state = self._parsed_state_or_create(connection, table_name, schema, **kw) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 2163, in _parsed_state_or_create info_cache=kw.get('info_cache', None) File "<string>", line 1, in <lambda> File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py", line 47, in cache ret = fn(self, con, *args, **kw) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 2188, in _setup_parser full_name=full_name) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 2275, in _show_create_table raise exc.NoSuchTableError(full_name) DatabaseNotControlledError: `migrate_version` Your help is much appreciated. Zong-Pei Han
By creating sand-boxed Python using virtualenv, "sh run.sh" runs fine. On Tue, 10 Dec 2013, zong-pei.han@imm.ox.ac.uk wrote: Date: Tue, 10 Dec 2013 10:01:56 From: zong-pei.han@imm.ox.ac.uk To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] The latest galaxy-dist run.sh failed Hi, We've just installed the latest galaxy-dist: hg clone https://bitbucket.org/galaxy/galaxy-dist/ cd galaxy-dist hg -v update stable The server runs: CentOS release 6.5, python 2.6.8, and mysql-5.1.71-1.el6.x86_64 "sh run.sh" has failed: ...... migrate.versioning.repository DEBUG 2013-12-10 09:35:51,145 Repository lib/galaxy/model/migrate loaded successfully migrate.versioning.repository DEBUG 2013-12-10 09:35:51,145 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_version', 'repository_id': 'Galaxy'}} galaxy.model.migrate.check DEBUG 2013-12-10 09:35:51,152 MySQL_python egg successfully loaded for mysql dialect galaxy.model.migrate.check INFO 2013-12-10 09:35:51,309 No database, initializing Traceback (most recent call last): File "/wwwdata/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/wwwdata/galaxy/lib/galaxy/app.py", line 54, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) File "/wwwdata/galaxy/lib/galaxy/model/migrate/check.py", line 64, in create_or_verify_database db_schema = schema.ControlledSchema( engine, migrate_repository ) File "/wwwdata/galaxy/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/schema.py", line 32, in __init__ self.load() File "/wwwdata/galaxy/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/schema.py", line 44, in load self.table = Table(tname, self.meta, autoload=True) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py", line 318, in __new__ table._init(name, metadata, *args, **kw) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py", line 381, in _init self._autoload(metadata, autoload_with, include_columns) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py", line 408, in _autoload self, include_columns, exclude_columns File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2425, in run_callable return conn.run_callable(callable_, *args, **kwargs) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1968, in run_callable return callable_(self, *args, **kwargs) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 260, in reflecttable return insp.reflecttable(table, include_columns, exclude_columns) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py", line 350, in reflecttable tbl_opts = self.get_table_options(table_name, schema, **table.kwargs) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py", line 178, in get_table_options **kw) File "<string>", line 1, in <lambda> File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py", line 47, in cache ret = fn(self, con, *args, **kw) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 2064, in get_table_options parsed_state = self._parsed_state_or_create(connection, table_name, schema, **kw) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 2163, in _parsed_state_or_create info_cache=kw.get('info_cache', None) File "<string>", line 1, in <lambda> File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py", line 47, in cache ret = fn(self, con, *args, **kw) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 2188, in _setup_parser full_name=full_name) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 2275, in _show_create_table raise exc.NoSuchTableError(full_name) DatabaseNotControlledError: `migrate_version` Your help is much appreciated. Zong-Pei Han ___________________________________________________________ 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/
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zong-pei.han＠imm.ox.ac.uk