Hi Greg,
 
I commented out sqlite line, but I missed "database_connection = " in the new 
line I added in the configuration file.
It is working now.
Thank you very much for the quick reply.
 
Cai

--- 12年4月24日,周二, Greg Von Kuster <g...@bx.psu.edu> 写道:


发件人: Greg Von Kuster <g...@bx.psu.edu>
主题: Re: [galaxy-dev] Galaxy with postgresql
收件人: "zhengqiu cai" <caizhq2...@yahoo.com.cn>
抄送: galaxy-dev@lists.bx.psu.edu
日期: 2012年4月24日,周二,上午2:08



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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