InnoDB can be set as default:

http://serverfault.com/questions/93559/how-do-i-set-the-default-table-type-as-innodb-in-my-cnf

It should also be the default storage engine if you are using MySQL 5.5 or higher:

http://dev.mysql.com/doc/refman/5.6/en/innodb-default-se.html

Which version of MySQL are you using? 5.5 / 5.6 are generally a lot nicer than e.g. 5.1

Dave T

From: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] On Behalf Of McCully, Dwayne (NIH/NIAMS) [C]
Sent: Friday, April 10, 2015 3:54 PM
To: 'galaxy-dev@lists.galaxyproject.org'
Subject: [galaxy-dev] MySQL InnoDB - Execution Order

Hello Everyone,

The running Galaxy in a production environment documentation states:

“If you are using MySQL with MyISAM table engine when Galaxy is in multiprocess configuration, workflow steps will get executed out of order and fail.

Use InnoDB engine instead or switch to PostgreSQL.”

I’ve enabled InnoDB for my MySQL database via the my.cnf file but the default database and database to log all database transactions were created with MyISAM files.

If this is normal, when will Galaxy create InnoDB tables? I don’t believe you can create a database with InnoDB.

Dwayne