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
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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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 <greg@bx.psu.edu> 写道： 发件人: Greg Von Kuster <greg@bx.psu.edu> 主题: Re: [galaxy-dev] Galaxy with postgresql 收件人: "zhengqiu cai" <caizhq2005@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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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