Hi,

We had some issues using MySQL instead of sqlite as well. This is how it was solved on our end (Fresh installation):

These steps are from a fresh Hg clone of galaxy (The latest version included the python egg needed for successful migration):

1) >sh setup.sh
2) Create a new MySQL database, in our case: galaxy-new
3) Create a MySQL user with sufficient privileges to talk to the created MySQL db, in our case: galaxy
4) In the galaxy root directory, edit the universe_wsgi.ini:  Uncomment the #database_connection line and edit it to this format:

database_connection = mysql://username:password@host/database_name

So in our case, it was:

mysql://galaxy@localhost/galaxy-new

If you have a password set for your MySQL user it would be: mysql://galaxy:yourpassword@localhost/galaxy-new

5) Save the file, and: > sh run.sh  
- From here the migration proceeded automatically.


Rgds,



Roy Weckiewicz.

On Thu, Mar 11, 2010 at 10:26 AM, Dijk, F van <f.van.dijk@medgen.umcg.nl> wrote:
Hi,
 
The syntax generated in the output generates errors. They look like this:
ERROR 1064 (42000) at line 1: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'TRANSACTION' at line 1
and
ERROR 1059 (42000) at line 77132: Identifier name 'ix_history_dataset_association_display_at_authorization_history_dataset_association_id' is too long
 
I hope this can be solved.
 
Sincerely,
 
 
Freerk
 
 

Van: Jeremy Goecks [mailto:jeremy.goecks@emory.edu]
Verzonden: donderdag 11 maart 2010 16:50
Aan: Dijk, F van; galaxy-dev

Onderwerp: Re: [galaxy-dev] Database migration problem

Hi Freerk,

Can you be more specific about the problems that you're seeing? Also, please continue to cc galaxy-dev as you're more likely to get help with your issues since it's going to a larger audience.

Thanks,
J.



On Mar 11, 2010, at 10:42 AM, Dijk, F van wrote:

Hi Jeremy,
 
Thanks for the fast replay. The first issue is solved, a new one occured during the second point. When I migrate the sqlite database to SQL and try to import it into the MySQL database some errors occur.
MySQL is complaining about the syntax used in the SQLdump.
We are using the following MySQL version:
mysql  Ver 14.12 Distrib 5.0.75, for debian-linux-gnu (x86_64) using readline 5.2
I also read the info on the link you provided in your answer, but this won't solve this problem I think. So, do you have a solution?
 
Sincerely,
 
 
Freerk van Dijk
 

Van: Jeremy Goecks [mailto:jeremy.goecks@emory.edu]
Verzonden: donderdag 11 maart 2010 15:25
Aan: Dijk, F van
CC: galaxy-dev@bx.psu.edu
Onderwerp: Re: [galaxy-dev] Database migration problem

Hi Freerk,

When we change the databaseconnection to "mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock" in the universe_wsgi.ini file and run Galaxy we receive an error like:

"Access denied for user 'root'@'localhost' (using password: NO)") None None

So is there an option somewhere which we also have to change to make the connection work?

You need to specify a username and password to access your database. Try this URL:

mysql://user:password@localhost/galaxy?unix_socket=/var/lib/mysql/mysql.sock
(exchanging 'user' and 'password' according to your settings)

And question two:
Do we need to migrate the content from the sqlite database to the MySQL database by hand or does this happen automatically?

You need to do the migration manually. Kanwei provided a nice solution to this problem a while back:


--
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.
--

Good luck and let us know if you have any more problems.

J.

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De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.

The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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--
Roy Weckiewicz
Texas A&M University