Hi Nate, I eventually gave up with the infobright server and used postgre instead (which worked just fine). I was playing with infobright to see if I could get some kind of connection between Galaxy and MedSavant (which uses an infobright server), or at least see if the connection would be possible with additional development. It's a project still in the back of my mind, but it has definitely moved very far down on my priority list at the moment. I've tweaked my Galaxy setup so much since this ticket was posted, I doubt if I could re-create the exact error without much effort. If I recall correctly, I don't think I did anything weird with the infobright or galaxy installation - a fresh install of each should give you the bug. As infobright-galaxy compatibility isn't high on my priority list anymore, I certainly don't expect you to waste much time with it. Thanks for the response! -Alex On Jan 23, 2012, at 1:10 PM, Nate Coraor wrote:
Hi Alex,
I'm taking a look at some bitbucket issues today and this is one of them. I'm wondering if you've figured anything out with this or are still having the same problems with MySQL. If you are, please let me know and I'll see if I can recreate it.
--nate
On Sep 15, 2011, at 5:00 PM, Greg Von Kuster wrote:
Alex,
I've created the following ticket for this issue as it looks to be a bug with Galaxy / mysql. You can follow the ticket to be aware of progress.
https://bitbucket.org/galaxy/galaxy-central/issue/660/galaxy-installation-wi...
Thanks for reporting this,
Greg Von Kuster
On Sep 14, 2011, at 7:35 PM, Alex R Bigelow wrote:
Hi, I am trying to install a local instance of Galaxy with an infobright mysql server; I created a database called "galaxy" (the user is also "galaxy," and it has all the privileges it should need), and the database_connection line is as follows:
database_connection = mysql://galaxy:***********@localhost/galaxy?unix_socket=/tmp/mysql-ib.sock
When I do this, I get the following error: Traceback (most recent call last): File "/gen21/alex/Apps/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/gen21/alex/Apps/galaxy-dist/lib/galaxy/app.py", line 32, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/gen21/alex/Apps/galaxy-dist/lib/galaxy/model/migrate/check.py", line 65, in create_or_verify_database db_schema = schema.ControlledSchema( engine, migrate_repository ) File "/gen21/alex/Apps/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py", line 24, in __init__ self._load() File "/gen21/alex/Apps/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py", line 36, in _load self.table = Table(tname, self.meta, autoload=True) File "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py", line 108, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py", line 236, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 1265, in reflecttable self.dialect.reflecttable(conn, table, include_columns) File "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py", line 1664, in reflecttable sql = self._show_create_table(connection, table, charset) File "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py", line 1835, in _show_create_table raise exc.NoSuchTableError(full_name) NoSuchTableError: migrate_version
I found this question in the archives: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-March/002216.html
As per both replies, I tried a virtual_env, which didn't work, and I also deleted the "galaxy" database so that it would create a fresh one, but, of course, now it can't connect to the database because it doesn't exist. How do I tell Galaxy to create the database it needs?
Thanks again for all the support, Alex Bigelow ___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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