Question: Converting to MySQL
gravatar for bravobih
4.5 years ago by
European Union
bravobih30 wrote:

When trying to start Galaxy with MySQL database instead of PostgresQL after several upgrades numbers on step 29 -> 30... Migration script to add column for a history slug. I get the following result (at the end of the trace):

File "/home/galaxy/galaxy-dist/eggs/MySQL_python-1.2.3c1_5.1.41_static-py2.6-linux-x86_64-ucs4.egg/MySQLdb/", line 36, in defaulterrorhandler
sqlalchemy.exc.OperationalError: (OperationalError) (1060, "Duplicate column name 'slug'") '\nALTER TABLE history ADD slug TEXT' ()

How can I get over this step?  Is there any DB structure that I can insert with mysqladmin or mysql ?

galaxy • 1.0k views
ADD COMMENTlink written 4.5 years ago by bravobih30


unfortunately, I have no clue about MySQL I just can recommend you to use PostgreSQL. MySQL has a few issues, especially with datatypes that seems to be problematic for a few users.

ADD REPLYlink written 4.5 years ago by Bjoern Gruening5.1k

(I'll first echo Bjoern in saying that Postgres is certainly preferred)

That said, starting with a fresh mysql database, this should not happen.  I'm setting up a mysql database now to test with, but can we get a few more details as well?  You said you're 'converting to mysql' in the title.  Does that mean you first manually migrated the data somehow?

ADD REPLYlink written 4.5 years ago by Dannon Baker3.7k
gravatar for Dannon Baker
4.5 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

Hey, I just wanted to follow up on this.  I'm unable to reproduce this with a fresh clone of galaxy-dist (latest) and a new mysql (mysql 5.5.37) database.  Are you still experiencing problems?  If not, can you detail what the fix was, for the benefit of others who may have similar issues?

ADD COMMENTlink written 4.5 years ago by Dannon Baker3.7k
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