Hi Kanwei,
Thank you for your response.
I've tried setting the database connection in the universe_wsgi.ini file to: database_connection = mysql:///galaxy?unix_socket=/private/tmp/mysql.sock (after a new download of galaxy and first running setup.sh) Is the format correct for a OSX system running OSX? -- When I try to 'sh run.sh' with this line included, I get the following errors:
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