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

 

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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:

http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-February/001996.html

--

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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