Fresh galaxy install fails to start

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

Fresh galaxy install fails to start

Iry Witham
Hi Dev Team,

I am attempting to get a new/clean installation running and am having difficulty.  I did a clone from and made my needed configuration changes for my environment.  I attempted to start it and needed to do the database upgrade via sh upgrade.  That went just fine.  I tried another start and got the following error:

migrate.versioning.repository DEBUG 2014-07-17 13:07:56,566 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_tools', 'repository_id': 'GalaxyTools'}}
tool_shed.galaxy_install.migrate.check DEBUG 2014-07-17 13:07:56,571 psycopg2 egg successfully loaded for postgres dialect
Traceback (most recent call last):
  File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/webapps/galaxy/", line 39, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/", line 46, in __init__
    self._configure_models( check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file )
  File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/", line 656, in _configure_models
    verify_tools( self, install_db_url, config_file, install_database_options )
  File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/migrate/", line 150, in verify_tools
    raise Exception( msg )

The list of files at the end of this message refers to tools that are configured to load into the tool panel for
this Galaxy instance, but have been removed from the Galaxy distribution.  These tools and their dependencies can be
automatically installed from the Galaxy tool shed at

To skip this process, attempt to start your Galaxy server again (e.g., sh or whatever you use).  If you do this,
be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should
be removed from your file named ./tool_conf.xml.

The location in which the tool repositories will be installed is the value of the 'tool_path' attribute in the <tool>
tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="../shed_tools">).  The default location
setting is '../shed_tools', which may be problematic for some cluster environments, so make sure to change it before
you execute the installation process if appropriate.  The configured location must be outside of the Galaxy installation
directory or it must be in a sub-directory protected by a properly configured .hgignore file if the directory is within
the Galaxy installation directory hierarchy.  This is because tool shed repositories will be installed using mercurial's
clone feature, which creates .hg directories and associated mercurial repository files.  Not having .hgignore properly
configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed
repositories if they are in directories that pose conflicts.  See mercurial's .hgignore documentation at the following
URL for details.

The following tool dependencies can also optionally be installed (see the option flag in the command below).  If you
choose to install them (recommended), they will be installed within the location specified by the 'tool_dependency_dir'
setting in your main Galaxy configuration file (e.g., uninverse_wsgi.ini).
Tool Dependency
Name: bx-python, Version: 0.7.1, Type: package

Tool Dependency
Name: R, Version: 2.11.0, Type: package

Tool Dependency
Name: rpy, Version: 1.0.3, Type: package

Tool Dependency
Name: numpy, Version: 1.7.1, Type: package

Tool Dependency
Name: yacca, Version: 1.0, Type: package

Tool Dependency
Name: kernlab, Version: 0.1-4, Type: package

Tool Dependency
Name: libxml2, Version: 2.9.1, Type: package

Tool Dependency
Name: libpng, Version: 1.6.7, Type: package

Tool Dependency
Name: fontconfig, Version: 2.11.1, Type: package

Tool Dependency
Name: blast+, Version: 2.2.26+, Type: package


/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/ SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed from 'postgres' to 'postgresql'. The new URL format is postgresql[+driver]://<user>:<pass>@<host>/<dbname>
sh ./scripts/migrate_tools/

The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies'
option to the above command like this:

sh ./scripts/migrate_tools/ install_dependencies

Tool dependencies can be installed after the repositories have been installed as well.

After the installation process finishes, you can start your Galaxy server.  As part of this installation process,
entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these
tools will continue to be loaded into your tool panel.  Because of this, existing entries for these tools have been
removed from your file named ./tool_conf.xml.


Removing PID file

I ignored that since it is related to a config file I copied from my previous instance.  I retried another start and I get the following:

migrate.versioning.repository DEBUG 2014-07-17 13:09:59,145 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_tools', 'repository_id': 'GalaxyTools'}}
tool_shed.galaxy_install.migrate.check DEBUG 2014-07-17 13:09:59,161 psycopg2 egg successfully loaded for postgres dialect
tool_shed.galaxy_install.migrate.check INFO 2014-07-17 13:09:59,215 At migrate_tools version 11
galaxy.model.orm DEBUG 2014-07-17 13:09:59,224 psycopg2 egg successfully loaded for postgres dialect
galaxy.config INFO 2014-07-17 13:09:59,251 Install database targetting Galaxy's database configuration.
sqlalchemy.pool.QueuePool WARNING 2014-07-17 13:10:01,869 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block

Traceback (most recent call last):
  File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/webapps/galaxy/", line 39, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/", line 52, in __init__
    self._configure_datatypes_registry( self.installed_repository_manager )
  File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/", line 605, in _configure_datatypes_registry
  File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/", line 278, in load_proprietary_datatypes
    .order_by( ):
  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/", line 2227, in __iter__
    return self._execute_and_instances(context)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/", line 2242, in _execute_and_instances
    result = conn.execute(querycontext.statement, self._params)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/", line 1449, in execute
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/", line 1584, in _execute_clauseelement
    compiled_sql, distilled_params
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/", line 1698, in _execute_context
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/", line 1691, in _execute_context
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/", line 331, in do_execute
    cursor.execute(statement, parameters)
ProgrammingError: (ProgrammingError) column tool_shed_repository.status does not exist
LINE 1: ...ist_to_shed AS tool_shed_repository_dist_to_shed, tool_shed_...
 'SELECT AS tool_shed_repository_id, tool_shed_repository.create_time AS tool_shed_repository_create_time, tool_shed_repository.update_time AS tool_shed_repository_update_time, tool_shed_repository.tool_shed AS tool_shed_repository_tool_shed, AS tool_shed_repository_name, tool_shed_repository.description AS tool_shed_repository_description, tool_shed_repository.owner AS tool_shed_repository_owner, tool_shed_repository.installed_changeset_revision AS tool_shed_repository_installed_changeset_revision, tool_shed_repository.changeset_revision AS tool_shed_repository_changeset_revision, tool_shed_repository.ctx_rev AS tool_shed_repository_ctx_rev, tool_shed_repository.metadata AS tool_shed_repository_metadata, tool_shed_repository.includes_datatypes AS tool_shed_repository_includes_datatypes, tool_shed_repository.tool_shed_status AS tool_shed_repository_tool_shed_status, tool_shed_repository.deleted AS tool_shed_repository_deleted, tool_shed_repository.uninstalled AS tool_shed_repository_uninstalled, tool_shed_repository.dist_to_shed AS tool_shed_repository_dist_to_shed, tool_shed_repository.status AS tool_shed_repository_status, tool_shed_repository.error_message AS tool_shed_repository_error_message \nFROM tool_shed_repository \nWHERE tool_shed_repository.includes_datatypes = %(includes_datatypes_1)s AND tool_shed_repository.deleted = %(deleted_1)s ORDER BY' {'includes_datatypes_1': True, 'deleted_1': False}
Removing PID file

Can someone point me to a resolution?

Iry T. Witham
Scientific Applications Administrator
Scientific Computing Group
Computational Sciences Dept.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609
Phone: 207-288-6744
email: iry.witham@...

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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:

To search Galaxy mailing lists use the unified search at: