I have installed a new Galaxy server utilizing the November 18,2011 
distribution on a SLES 11 VM and cannot get it to launch cleanly.  I am running 
postgreSQL v. 8.3.9 to create my database.  Once the database is created and 
running I launch my Galaxy server and within moments all of the PID fail except 
for the reports_webapp.pid.  When I tail the logs I find the following:

tail reports_webapp.log -
galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,179 Enabling 
'httpexceptions' middleware
galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,194 Enabling 
'recursive' middleware
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/Paste-1.6-py2.6.egg/paste/exceptions/serial_number_generator.py:11:
 DeprecationWarning: the md5 module is deprecated; use hashlib instead
  import md5
galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,272 Enabling 'error' 
middleware
galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,277 Enabling 'trans 
logger' middleware
galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,277 Enabling 'config' 
middleware
galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,294 Enabling 
'x-forwarded-host' middleware
Starting server in PID 20411.
serving on 0.0.0.0:9001 view at http://127.0.0.1:9001

tail web0.log -
galaxy.model.migrate.check DEBUG 2011-12-21 14:20:54,793 psycopg2 egg 
successfully loaded for postgres dialect
Traceback (most recent call last):
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/web/buildapp.py", 
line 82, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/app.py", 
line 39, in __init__
    create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( 
'__file__', None ), self.config.database_engine_options )
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/model/migrate/check.py",
 line 105, in create_or_verify_database
    % ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '38' but this code expects version '85'.  
Please backup your database and then migrate the schema by running 'sh 
manage_db.sh -c ./universe_wsgi.webapp.ini upgrade'.
Removing PID file web0.pid

tail runner0.log -
galaxy.model.migrate.check DEBUG 2011-12-21 14:20:54,789 psycopg2 egg 
successfully loaded for postgres dialect
Traceback (most recent call last):
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/web/buildapp.py", 
line 82, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/app.py", 
line 39, in __init__
    create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( 
'__file__', None ), self.config.database_engine_options )
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/model/migrate/check.py",
 line 105, in create_or_verify_database
    % ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '38' but this code expects version '85'.  
Please backup your database and then migrate the schema by running 'sh 
manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
Removing PID file runner0.pid


sh manage_db.sh upgrade -

38 -> 39...

Migration script to add a synopsis column to the library table.

Traceback (most recent call last):
  File "./scripts/manage_db.py", line 63, in <module>
    main( repository=repo, url=db_url )
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py",
 line 150, in main
    ret = command_func(**kwargs)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py",
 line 221, in upgrade
    return _migrate(url, repository, version, upgrade=True, err=err, **opts)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py",
 line 349, in _migrate
    schema.runchange(ver, change, changeset.step)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
 line 184, in runchange
    change.run(self.engine, step)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py",
 line 101, in run
    func()
  File 
"lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py",
 line 20, in upgrade
    c.create( Library_table )
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/changeset/schema.py",
 line 365, in create
    engine._run_visitor(visitorcallable, self, *args, **kwargs)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
 line 1158, in _run_visitor
    visitorcallable(self.dialect, conn, **kwargs).traverse(element)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py",
 line 89, in traverse
    return traverse(obj, self.__traverse_options__, self._visitor_dict)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py",
 line 200, in traverse
    return traverse_using(iterate(obj, opts), obj, visitors)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py",
 line 194, in traverse_using
    meth(target)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/changeset/ansisql.py",
 line 97, in visit_column
    self.execute()
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
 line 1812, in execute
    return self.connection.execute(self.buffer.getvalue())
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
 line 824, in execute
    return Connection.executors[c](self, object, multiparams, params)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
 line 888, in _execute_text
    return self.__execute_context(context)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
 line 896, in __execute_context
    self._cursor_execute(context.cursor, context.statement, 
context.parameters[0], context=context)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
 line 950, in _cursor_execute
    self._handle_dbapi_exception(e, statement, parameters, cursor, context)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
 line 931, in _handle_dbapi_exception
    raise exc.DBAPIError.instance(statement, parameters, e, 
connection_invalidated=is_disconnect)
sqlalchemy.exc.ProgrammingError: (ProgrammingError) column "synopsis" of 
relation "library" already exists
 '\nALTER TABLE "library"  ADD synopsis TEXT' {}

I have dropped the database multiple times and recreated it and intentionally 
left out steps when creating DB users and roles and the manage_db.sh fails at 
different spots.  However, I cannot get past 38 -> 39.  Any suggestions?

Thanks,

IRy
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