By creating sand-boxed Python using virtualenv, "sh run.sh"
runs fine.


On Tue, 10 Dec 2013, zong-pei....@imm.ox.ac.uk wrote:
Date: Tue, 10 Dec 2013 10:01:56
From: zong-pei....@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
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