Galaxy install error: NoSuchTableError: migrate_version
Hi, I've tried to install galaxy on my Ubuntu Linux amd64 2.6.27-11-generic, Python 2.5.2 (r252:60911), >>> sqlalchemy.__version__ '0.5.8', I ran $ hg clone http://bitbucket.org/galaxy/galaxy-central/ 5 days ago And I got this error after calling % sh run.sh Traceback (most recent call last): File "/home/tan/galaxy_dist/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/tan/galaxy_dist/lib/galaxy/app.py", line 28, in __init__ create_or_verify_database( db_url, self.config.database_engine_options ) File "/home/tan/galaxy_dist/lib/galaxy/model/migrate/check.py", line 66, in create_or_verify_database db_schema = schema.ControlledSchema( engine, migrate_repository ) File "/home/tan/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py", line 24, in __init__ self._load() File "/home/tan/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py", line 36, in _load self.table = Table(tname, self.meta, autoload=True) File "/var/lib/python-support/python2.5/sqlalchemy/schema.py", line 110, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/var/lib/python-support/python2.5/sqlalchemy/schema.py", line 226, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/var/lib/python-support/python2.5/sqlalchemy/engine/base.py", line 1275, in reflecttable self.dialect.reflecttable(conn, table, include_columns) File "/var/lib/python-support/python2.5/sqlalchemy/databases/sqlite.py", line 343, in reflecttable raise exceptions.NoSuchTableError(table.name) NoSuchTableError: migrate_version /var/lib/python-support/python2.5/sqlalchemy/__init__ says ver 0.4.6 Thanks, Patrick __________________________________________________________________ Connect with friends from any web browser - no download required. Try the new Yahoo! Canada Messenger for the Web BETA at http://ca.messenger.yahoo.com/webmessengerpromo.php
Hello Patrick, You should not be installing from the galaxy-central branch as it is the development branch and nothing is guaranteed to work. Instead, use the distribution branch at http://bitbucket.org/galaxy/galaxy-dist/. However, the behavior you saw is not due to your clone, but probably because you have an old database to which you have pointed your clone ( Galaxy versions older than rev 1464 will not include the migrate_version table ). If you don't need your old data, just drop your database and allow Galaxy to rebuild it at startup. If you want to keep your old data, you'll need to somehow manually migrate your database. Greg Von Kuster On Mar 14, 2010, at 5:03 PM, Patrick T. wrote:
Hi,
I've tried to install galaxy on my Ubuntu Linux amd64 2.6.27-11-generic, Python 2.5.2 (r252:60911), >>> sqlalchemy.__version__ '0.5.8', I ran $ hg clone http://bitbucket.org/galaxy/galaxy-central/ 5 days ago
And I got this error after calling % sh run.sh
Traceback (most recent call last): File "/home/tan/galaxy_dist/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/tan/galaxy_dist/lib/galaxy/app.py", line 28, in __init__ create_or_verify_database( db_url, self.config.database_engine_options ) File "/home/tan/galaxy_dist/lib/galaxy/model/migrate/check.py", line 66, in create_or_verify_database db_schema = schema.ControlledSchema( engine, migrate_repository ) File "/home/tan/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py", line 24, in __init__ self._load() File "/home/tan/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py", line 36, in _load self.table = Table(tname, self.meta, autoload=True) File "/var/lib/python-support/python2.5/sqlalchemy/schema.py", line 110, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/var/lib/python-support/python2.5/sqlalchemy/schema.py", line 226, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/var/lib/python-support/python2.5/sqlalchemy/engine/base.py", line 1275, in reflecttable self.dialect.reflecttable(conn, table, include_columns) File "/var/lib/python-support/python2.5/sqlalchemy/databases/sqlite.py", line 343, in reflecttable raise exceptions.NoSuchTableError(table.name) NoSuchTableError: migrate_version
/var/lib/python-support/python2.5/sqlalchemy/__init__ says ver 0.4.6
Thanks, Patrick
__________________________________________________________________ Connect with friends from any web browser - no download required. Try the new Yahoo! Canada Messenger for the Web BETA at http://ca.messenger.yahoo.com/webmessengerpromo.php _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
It looks like the NoSuchTableError may be misleading, since the following line references a locally installed version of sqlalchemy. The version conflict code clearly isn't working right and I am looking at it right now. Patrick, a workaround is to ensure that you're not using a python installation with locally installed 3rd-party modules, by setting up a clean environment using virtualenv and the --no-site-packages option: http://pypi.python.org/pypi/virtualenv --nate Greg Von Kuster wrote:
Hello Patrick,
You should not be installing from the galaxy-central branch as it is the development branch and nothing is guaranteed to work. Instead, use the distribution branch at http://bitbucket.org/galaxy/galaxy-dist/. However, the behavior you saw is not due to your clone, but probably because you have an old database to which you have pointed your clone ( Galaxy versions older than rev 1464 will not include the migrate_version table ). If you don't need your old data, just drop your database and allow Galaxy to rebuild it at startup. If you want to keep your old data, you'll need to somehow manually migrate your database.
Greg Von Kuster
On Mar 14, 2010, at 5:03 PM, Patrick T. wrote:
Hi,
I've tried to install galaxy on my Ubuntu Linux amd64 2.6.27-11-generic, Python 2.5.2 (r252:60911), >>> sqlalchemy.__version__ '0.5.8', I ran $ hg clone http://bitbucket.org/galaxy/galaxy-central/ 5 days ago
And I got this error after calling % sh run.sh
Traceback (most recent call last): File "/home/tan/galaxy_dist/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/tan/galaxy_dist/lib/galaxy/app.py", line 28, in __init__ create_or_verify_database( db_url, self.config.database_engine_options ) File "/home/tan/galaxy_dist/lib/galaxy/model/migrate/check.py", line 66, in create_or_verify_database db_schema = schema.ControlledSchema( engine, migrate_repository ) File "/home/tan/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py", line 24, in __init__ self._load() File "/home/tan/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py", line 36, in _load self.table = Table(tname, self.meta, autoload=True) File "/var/lib/python-support/python2.5/sqlalchemy/schema.py", line 110, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/var/lib/python-support/python2.5/sqlalchemy/schema.py", line 226, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/var/lib/python-support/python2.5/sqlalchemy/engine/base.py", line 1275, in reflecttable self.dialect.reflecttable(conn, table, include_columns) File "/var/lib/python-support/python2.5/sqlalchemy/databases/sqlite.py", line 343, in reflecttable raise exceptions.NoSuchTableError(table.name) NoSuchTableError: migrate_version
/var/lib/python-support/python2.5/sqlalchemy/__init__ says ver 0.4.6
Thanks, Patrick
__________________________________________________________________ Connect with friends from any web browser - no download required. Try the new Yahoo! Canada Messenger for the Web BETA at http://ca.messenger.yahoo.com/webmessengerpromo.php _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Thanks Greg and Nate. It worked after using virtualenv as Nate suggested. $ virtualenv --not-site-packages ENV $ export PATH=$HOME/ENV/bin:$PATH $ ./run.sh Patrick --- On Mon, 3/15/10, Nate Coraor <nate@bx.psu.edu> wrote:
From: Nate Coraor <nate@bx.psu.edu> Subject: Re: [galaxy-dev] Galaxy install error: NoSuchTableError: migrate_version To: "Greg Von Kuster" <greg@bx.psu.edu> Cc: "Patrick T." <ppatrickt@yahoo.com>, galaxy-dev@bx.psu.edu Received: Monday, March 15, 2010, 11:33 AM It looks like the NoSuchTableError may be misleading, since the following line references a locally installed version of sqlalchemy. The version conflict code clearly isn't working right and I am looking at it right now.
Patrick, a workaround is to ensure that you're not using a python installation with locally installed 3rd-party modules, by setting up a clean environment using virtualenv and the --no-site-packages option:
http://pypi.python.org/pypi/virtualenv
--nate
Hello Patrick,
You should not be installing from the galaxy-central branch as it is the development branch and nothing is guaranteed to work. Instead, use the distribution branch at http://bitbucket.org/galaxy/galaxy-dist/. However, the behavior you saw is not due to your clone, but
Greg Von Kuster
On Mar 14, 2010, at 5:03 PM, Patrick T. wrote:
Hi,
I've tried to install galaxy on my Ubuntu Linux amd64 2.6.27-11-generic, Python 2.5.2 (r252:60911),
sqlalchemy.__version__ '0.5.8', I ran $ hg clone http://bitbucket.org/galaxy/galaxy-central/ 5 days ago
And I got this error after calling % sh run.sh
Traceback (most recent call last): File "/home/tan/galaxy_dist/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/tan/galaxy_dist/lib/galaxy/app.py", line 28, in __init__ create_or_verify_database( db_url, self.config.database_engine_options ) File "/home/tan/galaxy_dist/lib/galaxy/model/migrate/check.py",
db_schema = schema.ControlledSchema( engine, migrate_repository ) File "/home/tan/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py",
self._load() File "/home/tan/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py",
self.table = Table(tname, self.meta, autoload=True) File "/var/lib/python-support/python2.5/sqlalchemy/schema.py",
return type.__call__(self, name,
File "/var/lib/python-support/python2.5/sqlalchemy/schema.py",
_bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/var/lib/python-support/python2.5/sqlalchemy/engine/base.py",
self.dialect.reflecttable(conn,
File "/var/lib/python-support/python2.5/sqlalchemy/databases/sqlite.py",
Greg Von Kuster wrote: probably because you have an old database to which you have pointed your clone ( Galaxy versions older than rev 1464 will not include the migrate_version table ). If you don't need your old data, just drop your database and allow Galaxy to rebuild it at startup. If you want to keep your old data, you'll need to somehow manually migrate your database. line 66, in create_or_verify_database line 24, in __init__ line 36, in _load line 110, in __call__ metadata, *args, **kwargs) line 226, in __init__ line 1275, in reflecttable table, include_columns) line 343, in reflecttable
raise exceptions.NoSuchTableError(table.name) NoSuchTableError: migrate_version
/var/lib/python-support/python2.5/sqlalchemy/__init__ says ver 0.4.6
Thanks, Patrick
Connect with friends from any web browser - no download required. Try the new Yahoo! Canada Messenger for the Web BETA at http://ca.messenger.yahoo.com/webmessengerpromo.php _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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Patrick T. wrote:
Thanks Greg and Nate. It worked after using virtualenv as Nate suggested.
$ virtualenv --not-site-packages ENV $ export PATH=$HOME/ENV/bin:$PATH $ ./run.sh
Patrick
Hi Patrick, I'm glad the workaround fixes it for you. It should also be fixed properly in changeset 3537:2fa5488a9b3e, which I just committed to our development repo (it should be available in our public repo in a few days). --nate
--- On Mon, 3/15/10, Nate Coraor <nate@bx.psu.edu> wrote:
From: Nate Coraor <nate@bx.psu.edu> Subject: Re: [galaxy-dev] Galaxy install error: NoSuchTableError: migrate_version To: "Greg Von Kuster" <greg@bx.psu.edu> Cc: "Patrick T." <ppatrickt@yahoo.com>, galaxy-dev@bx.psu.edu Received: Monday, March 15, 2010, 11:33 AM It looks like the NoSuchTableError may be misleading, since the following line references a locally installed version of sqlalchemy. The version conflict code clearly isn't working right and I am looking at it right now.
Patrick, a workaround is to ensure that you're not using a python installation with locally installed 3rd-party modules, by setting up a clean environment using virtualenv and the --no-site-packages option:
http://pypi.python.org/pypi/virtualenv
--nate
Hello Patrick,
You should not be installing from the galaxy-central branch as it is the development branch and nothing is guaranteed to work. Instead, use the distribution branch at http://bitbucket.org/galaxy/galaxy-dist/. However, the behavior you saw is not due to your clone, but
Greg Von Kuster
On Mar 14, 2010, at 5:03 PM, Patrick T. wrote:
Hi,
I've tried to install galaxy on my Ubuntu Linux amd64 2.6.27-11-generic, Python 2.5.2 (r252:60911),
sqlalchemy.__version__ '0.5.8', I ran $ hg clone http://bitbucket.org/galaxy/galaxy-central/ 5 days ago
And I got this error after calling % sh run.sh
Traceback (most recent call last): File "/home/tan/galaxy_dist/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/tan/galaxy_dist/lib/galaxy/app.py", line 28, in __init__ create_or_verify_database( db_url, self.config.database_engine_options ) File "/home/tan/galaxy_dist/lib/galaxy/model/migrate/check.py",
db_schema = schema.ControlledSchema(
engine, migrate_repository )
File "/home/tan/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py",
self._load() File
"/home/tan/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py",
self.table = Table(tname, self.meta,
autoload=True)
File "/var/lib/python-support/python2.5/sqlalchemy/schema.py",
return type.__call__(self, name,
File "/var/lib/python-support/python2.5/sqlalchemy/schema.py",
_bind_or_error(metadata).reflecttable(self, include_columns=include_columns)
File "/var/lib/python-support/python2.5/sqlalchemy/engine/base.py",
self.dialect.reflecttable(conn,
File "/var/lib/python-support/python2.5/sqlalchemy/databases/sqlite.py",
Greg Von Kuster wrote: probably because you have an old database to which you have pointed your clone ( Galaxy versions older than rev 1464 will not include the migrate_version table ). If you don't need your old data, just drop your database and allow Galaxy to rebuild it at startup. If you want to keep your old data, you'll need to somehow manually migrate your database. line 66, in create_or_verify_database line 24, in __init__ line 36, in _load line 110, in __call__ metadata, *args, **kwargs) line 226, in __init__ line 1275, in reflecttable table, include_columns) line 343, in reflecttable
raise
exceptions.NoSuchTableError(table.name)
NoSuchTableError: migrate_version
/var/lib/python-support/python2.5/sqlalchemy/__init__ says ver 0.4.6
Thanks, Patrick
Connect with friends from any web browser - no download required. Try the new Yahoo! Canada Messenger for the Web BETA at http://ca.messenger.yahoo.com/webmessengerpromo.php _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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participants (3)
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Greg Von Kuster -
Nate Coraor -
Patrick T.