Hi Cal,

Did you comment out this line?

# By default, Galaxy uses a SQLite database found here

#database_file = database/universe.sqlite

Also, I assume you following reference:

in Galaxy configuration file, use postgresql
postgres:///galaxy_db?user=ubuntu&host=/var/run/postgresql

actually looks like this in your config file:

database_connection = postgres:///galaxy_db?user=ubuntu&host=/var/run/postgresql

Greg Von Kuster

On Apr 23, 2012, at 2:03 PM, zhengqiu cai wrote:

Hi All,

I want to use postgresql instead of sqlite, and below is how I did the settings:

I am running Galaxy under the user ubuntu, so first I create the ubuntu user
sudo -u postgres createuser -D -A -P ubuntu

Then I create the database named galaxy_db
sudo -u postgres createdb -O ubuntu galaxy_db

in Galaxy configuration file, use postgresql
postgres:///galaxy_db?user=ubuntu&host=/var/run/postgresql

When I start Galaxy, sqlite dialect, not postgresql is selected. I am pasting part of the log below:
galaxy.model.migrate.check DEBUG 2012-04-23 17:59:52,676 pysqlite>=2 egg successfully loaded for sqlite dialect
galaxy.model.migrate.check INFO 2012-04-23 17:59:52,707 At database version 93
galaxy.tool_shed.migrate.check DEBUG 2012-04-23 17:59:52,718 pysqlite>=2 egg successfully loaded for sqlite dialect
galaxy.tool_shed.migrate.check INFO 2012-04-23 17:59:52,730 At migrate_tools version 1
galaxy.model.custom_types DEBUG 2012-04-23 17:59:52,735 pysqlite>=2 egg successfully loaded for sqlite dialect

Is there anything wrong with my configuration?

Thank you.

Cai

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