Thanks!  I did hg pull -u. For the database, I downgraded to 108 and then
upgraded again but got this error when upgrading.  Is it due to the Ubuntu
bug?  Or something else?  Should I be sticking with a particular Hg version
instead of the latest?

$ sh upgrade
115 -> 116...

Tables for a next generation sequencing lims tied to requests.

SAWarning: Did not recognize type 'BIGINT' of column 'bytes'
Traceback (most recent call last):
  File "./scripts/", line 65, in <module>
    main( repository=repo, url=db_url )
line 207, in main
    ret = command_func(**kwargs)
line 186, in upgrade
    return _migrate(url, repository, version, upgrade=True, err=err, **opts)
  File "<string>", line 2, in _migrate
line 159, in with_engine
    return f(*a, **kw)
line 366, in _migrate
    schema.runchange(ver, change, changeset.step)
line 91, in runchange, step)
line 145, in run
  File "lib/galaxy/model/migrate/versions/", line 52, in
    for table in _get_tables(metadata):
  File "lib/galaxy/model/migrate/versions/", line 34, in
    primary_key = True),
  File "build/bdist.linux-x86_64/egg/sqlalchemy/", line 305, in
sqlalchemy.exc.InvalidRequestError: Table 'sample_request_map' is already
defined for this MetaData instance.  Specify 'extend_existing=True' to
redefine options and columns on an existing Table object.

On Tue, Jul 2, 2013 at 10:59 AM, Dannon Baker <>wrote:

> On Mon, Jul 1, 2013 at 8:34 PM, Brad Chapman <> wrote:
>> This was a typo in the downgrade function for one of the patches. I
>> pushed a fix so if you update from bitbucket things should work smoothly
>> again (once we get to problem 2 below).
>> For anyone with galaxy-dist commit privileges, here's the one liner:
> Thanks Brad, added to stable branch in

Lee Katz, Ph.D.
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