galaxy.model.migrate.check DEBUG 2010-02-18 18:15:06,092 MySQL_python egg successfully loaded for mysql dialect

Traceback (most recent call last):

File "/Users/rsw3284/Downloads/galaxy-NEW/lib/galaxy/web/buildapp.py", line 61, in app_factory

app = UniverseApplication( global_conf = global_conf, **kwargs )

File "/Users/rsw3284/Downloads/galaxy-NEW/lib/galaxy/app.py", line 28, in __init__

create_or_verify_database( db_url, self.config.database_engine_options )

File "/Users/rsw3284/Downloads/galaxy-NEW/lib/galaxy/model/migrate/check.py", line 50, in create_or_verify_database

engine = create_engine( url, **engine_options )

File "/Users/rsw3284/Downloads/galaxy-NEW/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/__init__.py", line 223, in create_engine

return strategy.create(*args, **kwargs)

File "/Users/rsw3284/Downloads/galaxy-NEW/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/strategies.py", line 62, in create

dbapi = dialect_cls.dbapi(**dbapi_args)

File "/Users/rsw3284/Downloads/galaxy-NEW/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/mysql.py", line 1456, in dbapi

import MySQLdb as mysql

File "/Users/rsw3284/Downloads/galaxy-NEW/eggs/py2.5-macosx-10.3-fat-ucs2/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat.egg/MySQLdb/__init__.py", line 19, in <module>

File "/Users/rsw3284/Downloads/galaxy-NEW/eggs/py2.5-macosx-10.3-fat-ucs2/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat.egg/_mysql.py", line 7, in <module>

File "/Users/rsw3284/Downloads/galaxy-NEW/eggs/py2.5-macosx-10.3-fat-ucs2/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat.egg/_mysql.py", line 6, in __bootstrap__

ImportError: dlopen(/Users/rsw3284/.python-eggs/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat.egg-tmp/_mysql.so, 2): Library not loaded: /afs/bx.psu.edu/home/nate/work/galaxy_central/scripts/scramble/build/py2.4-macosx-10.3-fat-ucs2/MySQL_python/mysql/lib/mysql/libmysqlclient_r.15.dylib

Referenced from: /Users/rsw3284/.python-eggs/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat.egg-tmp/_mysql.so

Reason: image not found

The program fails here and no database file is ever created. If I run the program with the previously mentioned line commented, the sqlite database creation goes without a hitch, but once exported the syntax is much different from what mysql will accept. Any ideas?

Rgds,

Roy Weckiewicz

On Thu, Feb 18, 2010 at 2:56 PM, Kanwei Li <kanwei@gmail.com> wrote:

Hi Roy,

What I would suggest is to dump the sqlite database to standard sql,
and then creating a new instance of galaxy that has mysql as the
configured database. When you run the setup and run script, you'll
have a freshly instantiated galaxy with empty mysql tables. Then you
can just import the standard sql file into the mysql database.

Hope this helps,

Kanwei

On Thu, Feb 18, 2010 at 1:27 PM, Roy Weckiewicz <roystefan@gmail.com> wrote:
> Hello,
> I am trying to configure a local galaxy server using a MYSQL database
> instead of the standard sqlite3. I'm using OSX and have been attempting
> (unsuccessfully) to convert the sqlite database (universe.sql) to mysql
> format. Basically, I am in need of the database table schema for mysql. I
> noticed on your web page that you host a mysql server
> at: genome-mysql.cse.ucsc.edu
> -- would it be possible to do some sort of mysqldump or mysqlhotcopy in
> order to download the table schema, so that I could upload them into my
> local mysql installation?
>
> I've tried using Sqlite3 to dump the contents of universe.sql, but
> there are numerous syntax differences that need to be addressed
> before it will load successfully into my mysql database.
> Do you have any suggestions on how to either migrate the database from
> sqlite3 to MYSQL (via script or program),
> or create the mysql database from scratch and just import the correct table
> schema?
>
> Any help would be appreciated.
>
> MYSQL: Ver 14.14 Distrib 5.1.37, for apple-darwin9.5.0 (i386) using readline
> 5.1
> Python 2.5.1
>
>
> Rgds,
>
>
> Roy Weckiewicz.
>
> --
> Roy Weckiewicz
> Texas A&M University
>

> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
>

--
Roy Weckiewicz
Texas A&M University