Your database is not cleanly dropped when you start up your Galaxy server  - 
notice all of the migration scripts that fail because table columns, etc 
already exist.  Here's an example:

> 0012_user_address DEBUG 2011-12-14 15:15:12,085 Adding column 'deleted' to
> request_type table failed: (ProgrammingError) column "deleted" of relation
> "request_type" already exists


On Jan 3, 2012, at 11:59 AM, Iry Witham wrote:

> Hi Nate,
> 
>       I do not create any tables manually.  I simply create the database and
> setup users and roles.  I do the following:
> 
> initdb ­D /local/postgresql/data
> pg_ctl ­D /local/postgresql/data ­I /local/postgresql/pgsql.log start
> createdb galaxy_1
> 
> 
> Sudo su - postgres
> pgsql galaxy_1
> CREATE USER galaxy
> CREATE USER galaxyftp
> ALTER ROLE galaxyftp PASSWORD 'dbpassword'
> GRANT SELECT ON galaxy_user TO galaxyftp (Note: this fails prior to
> launching galaxy server for the first time)
> 
> I start galaxy and run 'sh manage_db.sh upgrade'.
> 
> 0 -> 1... 
> done
> 1 -> 2... 
> done
> 2 -> 3... 
> done
> 3 -> 4... 
> done
> 4 -> 5... 
> done
> 5 -> 6... 
> ========================================
> This migration script changes certain values in the
> history_dataset_association.extension
> column, specifically 'qual' is chaged to be 'qual454'.
> ========================================
> /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_
> r6498-py2.6.egg/sqlalchemy/sql/compiler.py:336: SAWarning: The SQLAlchemy
> psycopg2 dialect now automatically escapes '%' in text() expressions to
> '%%'.
>  BIND_PARAMS.sub(do_bindparam, self.post_process_text(textclause.text))
> done
> 6 -> 7... 
> ========================================
> This migration script creates the new history_user_share_association
> table, and adds
> a new boolean type column to the history table.  This provides support for
> sharing
> histories in the same way that workflows are shared.
> ========================================
> done
> 7 -> 8... 
> ========================================
> This migration script adds the following new tables for supporting Galaxy
> forms:
> 1) form_definition_current
> 2) form_definition
> 3) form_values
> 4) request_type
> 5) request
> 6) sample
> 7) sample_state
> 8) sample_event
> ========================================
> done
> 8 -> 9... 
> ========================================
> This migration script adds a new column to 2 tables:
> 1) a new boolean type column named 'submitted' to the 'request' table
> 2) a new string type column named 'bar_code' to the 'sample' table
> ========================================
> done
> 9 -> 10... 
> ========================================
> This migration script adds the
> history_dataset_association_display_at_authorization table, which
> allows 'private' datasets to be displayed at external sites without making
> them public.
> 
> If using mysql, this script will display the following error, which is
> corrected in the next migration
> script: history_dataset_association_display_at_authorization table failed:
> (OperationalError)
> (1059, 'Identifier name
> 'ix_history_dataset_association_display_at_authorization_update_time'
> is too long.
> ========================================
> done
> 10 -> 11... 
> ========================================
> This script fixes a problem introduced in the previous migration script (
> 9->10 ).  MySQL
> has a name length limit and thus the index
> 'ix_hdadaa_history_dataset_association_id' has
> to be manually created.
> ========================================
> done
> 11 -> 12... 
> ========================================
> This script adds a new user_address table that is currently only used with
> sample requests, where
> a user can select from a list of his addresses to associate with the
> request.  This script also
> drops the request.submitted column which was boolean and replaces it with
> a request.state column
> which is a string, allowing for more flexibility with request states.
> ========================================
> 0012_user_address DEBUG 2011-12-14 15:15:12,085 Adding column 'deleted' to
> request_type table failed: (ProgrammingError) column "deleted" of relation
> "request_type" already exists
> '\nALTER TABLE "request_type"  ADD deleted BOOLEAN' {}
> 0012_user_address DEBUG 2011-12-14 15:15:12,085 Adding column 'deleted' to
> request_type table failed: (ProgrammingError) column "deleted" of relation
> "request_type" already exists
> '\nALTER TABLE "request_type"  ADD deleted BOOLEAN' {}
> done
> 12 -> 13... 
> ========================================
> This migration script eliminates all of the tables that were used for the
> 1st version of the
> library templates where template fields and contents were each stored as a
> separate table row
> in various library item tables.  All of these tables are dropped in this
> script, eliminating all
> existing template data.  A total of 14 existing tables are dropped.
> 
> We're now basing library templates on Galaxy forms, so field contents are
> stored as a jsonified
> list in the form_values table.  This script introduces the following 3 new
> association tables:
> 1) library_info_association
> 2) library_folder_info_association
> 3) library_dataset_dataset_info_association
> 
> If using mysql, this script will throw an (OperationalError) exception due
> to a long index name
> on the library_dataset_dataset_info_association table, which is OK because
> the script creates
> an index with a shortened name.
> ========================================
> done
> 13 -> 14... 
> 
> Migration script to add support for "Pages".
>  1) Creates Page and PageRevision tables
>  2) Adds username column to User table
> 
> done
> 14 -> 15... 
> 
> This migration script adds the tables necessary to support tagging of
> histories,
> datasets, and history-dataset associations (user views of datasets).
> 
> If using mysql, this script will display the following error, which is
> corrected in the next migration script:
> history_dataset_association_tag_association table failed:
> (OperationalError) (1059, 'Identifier name
> 'ix_history_dataset_association_tag_association_history_dataset_association
> _id'
> is too long)
> (ProgrammingError) relation "tag" already exists
> '\nCREATE TABLE tag (\n\tid SERIAL NOT NULL, \n\ttype INTEGER,
> \n\tparent_id INTEGER, \n\tname VARCHAR(255), \n\tPRIMARY KEY (id), \n\t
> FOREIGN KEY(parent_id) REFERENCES tag (id), \n\t UNIQUE (name)\n)\n\n' {}
> done
> 15 -> 16... 
> 
> This script fixes a problem introduced in 0015_tagging.py.  MySQL has a
> name length limit and thus the index
> 'ix_hda_ta_history_dataset_association_id'
> has to be manually created.
> done
> 16 -> 17... 
> ========================================
> This script adds 3 indexes to table columns: library_folder.name,
> library_dataset.name, library_dataset_dataset_association.name.
> ========================================
> 0017_library_item_indexes DEBUG 2011-12-14 15:15:15,400 Adding index
> 'ix_library_folder_name' to library_folder table failed:
> (ProgrammingError) relation "ix_library_folder_name" already exists
> 'CREATE INDEX ix_library_folder_name ON library_folder (name)' {}
> 0017_library_item_indexes DEBUG 2011-12-14 15:15:15,400 Adding index
> 'ix_library_folder_name' to library_folder table failed:
> (ProgrammingError) relation "ix_library_folder_name" already exists
> 'CREATE INDEX ix_library_folder_name ON library_folder (name)' {}
> 0017_library_item_indexes DEBUG 2011-12-14 15:15:15,413 Adding index
> 'ix_library_dataset_name' to library_dataset table failed:
> (ProgrammingError) relation "ix_library_dataset_name" already exists
> 'CREATE INDEX ix_library_dataset_name ON library_dataset (name)' {}
> 0017_library_item_indexes DEBUG 2011-12-14 15:15:15,413 Adding index
> 'ix_library_dataset_name' to library_dataset table failed:
> (ProgrammingError) relation "ix_library_dataset_name" already exists
> 'CREATE INDEX ix_library_dataset_name ON library_dataset (name)' {}
> done
> 17 -> 18... 
> 
> This migration script provides support for (a) ordering tags by recency and
> (b) tagging pages. This script deletes all existing tags.
> done
> 18 -> 19... 
> ========================================
> This script creates a request.folder_id column which is a foreign
> key to the library_folder table. This also adds a 'type' and 'layout'
> column
> to the form_definition table.
> ========================================
> 0019_request_library_folder DEBUG 2011-12-14 15:15:16,933 Adding column
> 'type' to form_definition table failed: (ProgrammingError) column "type"
> of relation "form_definition" already exists
> '\nALTER TABLE "form_definition"  ADD type VARCHAR(255)' {}
> 0019_request_library_folder DEBUG 2011-12-14 15:15:16,933 Adding column
> 'type' to form_definition table failed: (ProgrammingError) column "type"
> of relation "form_definition" already exists
> '\nALTER TABLE "form_definition"  ADD type VARCHAR(255)' {}
> 0019_request_library_folder DEBUG 2011-12-14 15:15:16,934 Adding column
> 'layout' to form_definition table failed: (ProgrammingError) column
> "layout" of relation "form_definition" already exists
> '\nALTER TABLE "form_definition"  ADD layout BYTEA' {}
> 0019_request_library_folder DEBUG 2011-12-14 15:15:16,934 Adding column
> 'layout' to form_definition table failed: (ProgrammingError) column
> "layout" of relation "form_definition" already exists
> '\nALTER TABLE "form_definition"  ADD layout BYTEA' {}
> done
> 19 -> 20... 
> 
> ========================================
> This script creates a job_to_output_library_dataset table for allowing
> library
> uploads to run as regular jobs.  To support this, a library_folder_id
> column is
> added to the job table, and library_folder/output_library_datasets
> relations
> are added to the Job object.  An index is also added to the dataset.state
> column.
> ========================================
> done
> 20 -> 21... 
> 
> This migration script adds a user preferences table to Galaxy.
> 
> done
> 21 -> 22... 
> 
> Migration script to add support for storing visualizations.
>  1) Creates Visualization and VisualizationRevision tables
> 
> done
> 22 -> 23... 
> 
> Migration script to add columns for tracking whether pages are deleted and
> publicly accessible.
> 
> done
> 23 -> 24... 
> 
> Remove unique constraint from page slugs to allow creating a page with
> the same slug as a deleted page.
> 
> done
> 24 -> 25... 
> ========================================
> This script adds a foreign key to the form_values table in the galaxy_user
> table
> ========================================
> done
> 25 -> 26... 
> 
> ========================================
> This script adds tables needed for Galaxy cloud functionality.
> ========================================
> done
> 26 -> 27... 
> ========================================
> This migration script adds the request_event table and
> removes the state field in the request table
> ========================================
> done
> 27 -> 28... 
> ========================================
> This script adds the filename_override_metadata column to the
> JobExternalOutputMetadata table,
> allowing existing metadata files to be written when using external
> metadata and a cluster
> set up with read-only access to database/files
> ========================================
> done
> 28 -> 29... 
> 
> This migration script adds a user actions table to Galaxy.
> 
> done
> 29 -> 30... 
> 
> Migration script to add column for a history slug.
> 
> done
> 30 -> 31... 
> 
> Migration script to (a) add and populate necessary columns for doing
> community tagging of histories, datasets, and pages and (b) add table for
> doing individual and community tagging of workflows.
> 
> SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so this script will
> generate error messages when run against SQLite; however, script does
> execute successfully against SQLite.
> 
> done
> 31 -> 32... 
> 
> Migration script to add slug column for stored workflow.
> 
> done
> 32 -> 33... 
> 
> Migration script to add necessary columns for distinguishing between
> viewing/importing and publishing histories, workflows, and pages. Script
> adds published column to histories and workflows and importable column to
> pages.
> 
> done
> 33 -> 34... 
> 
> Migration script to create a table for page-user share association.
> 
> done
> 34 -> 35... 
> 
> Migration script to (a) create tables for annotating objects and (b)
> create tags for workflow steps.
> 
> done
> 35 -> 36... 
> 
> Migration script to add a deleted column to the following tables:
> library_info_association, library_folder_info_association,
> library_dataset_dataset_info_association.
> 
> done
> 36 -> 37... 
> 
> This migration script removes the library_id & folder_id fields in the
> 'request' table and
> adds the same to the 'sample' table. This also adds a 'datatx' column to
> request_type table 
> to store the sequencer login information. Finally, this adds a
> 'dataset_files' column to
> the sample table. 
> 
> done
> 37 -> 38... 
> 
> Migration script to add an inheritable column to the following tables:
> library_info_association, library_folder_info_association.
> Also, in case of sqlite check if the previous migration script deleted the
> request table and if so, restore the table.
> 
> done
> 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_tabl
> e.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' {}
> 
> Thanks,
> Iry
> 
> 
> 
> 
> 
> On 1/3/12 11:41 AM, "Nate Coraor" <n...@bx.psu.edu> wrote:
> 
>> On Dec 21, 2011, at 2:49 PM, Iry Witham wrote:
>> 
>>> 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/migrat
>>> e/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/migrat
>>> e/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_ta
>>> ble.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_d
>>> ev_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_d
>>> ev_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_d
>>> ev_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_d
>>> ev_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_d
>>> ev_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_d
>>> ev_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_d
>>> ev_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_d
>>> ev_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_d
>>> ev_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_d
>>> ev_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?
>> 
>> Hi Iry,
>> 
>> Can you clarify whether you are manually creating any tables?  You only
>> need to create the database itself, Galaxy handles all of the tables.
>> 
>> If you're not creating any tables, what is the output of the very first
>> run of Galaxy on an empty database?
>> 
>> --nate
>> 
>>> 
>>> Thanks,
>>> 
>>> IRy
>>> ___________________________________________________________
>>> 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/
>> 
> 
> <default.xml>___________________________________________________________
> 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/

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu




___________________________________________________________
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/

Reply via email to