Re: [galaxy-dev] [galaxy-user] (OperationalError) unable to open database file
On Dec 29, 2011, at 12:15 AM, Cai Shaojiang wrote:
Dear friends,
We are trying to install galaxy on the server (ubuntu 11), just by following the steps on the page "Get Galaxy: Galaxy Download and Installation" of galaxy wiki. But when we start running it, it shows the following error message.
OperationalError: (OperationalError) unable to open database file u'INSERT INTO galaxy_session (create_time, update_time, user_id, remote_host, remote_addr, referer, current_history_id, session_key, is_valid, prev_session_id, disk_usage) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)' ['2011-12-29 04:52:46.575702', '2011-12-29 04:52:46.575719', None, '10.50.70.45', '10.50.70.45', None, None, '5a38b2a7e6d77a7145726cb0881eadf6', 1, None, None]
It seems something wrong with the write permission. Could you give any hint where the problem could be? Thanks.
Hi Cai, I've moved this over to the galaxy-dev list since it pertains to a local installation. Please make sure that the galaxy-dist/database/ directory is writable by the user running the Galaxy server. Also, if you plan to use this server for anything other than single-user development, I would suggest switching to a PostgreSQL server. This is trivial on Ubuntu (apt-get install postgresql, createuser/createdb, then edit universe_wsgi.ini as described at http://usegalaxy.org/production ). --ndate
Best regards.
Yours: Cai ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Thanks, Nate, I now switched to MySQL, and the problem disappeared. Thanks. The manual highly recommend postgresql, is there any critical point to use it, instead of mysql? I am just more familiar with mysql. Thanks. On Wed, Jan 4, 2012 at 1:58 AM, Nate Coraor <nate@bx.psu.edu> wrote:
On Dec 29, 2011, at 12:15 AM, Cai Shaojiang wrote:
Dear friends,
We are trying to install galaxy on the server (ubuntu 11), just by following the steps on the page "Get Galaxy: Galaxy Download and Installation" of galaxy wiki. But when we start running it, it shows the following error message.
OperationalError: (OperationalError) unable to open database file u'INSERT INTO galaxy_session (create_time, update_time, user_id, remote_host, remote_addr, referer, current_history_id, session_key, is_valid, prev_session_id, disk_usage) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)' ['2011-12-29 04:52:46.575702', '2011-12-29 04:52:46.575719', None, '10.50.70.45', '10.50.70.45', None, None, '5a38b2a7e6d77a7145726cb0881eadf6', 1, None, None]
It seems something wrong with the write permission. Could you give any hint where the problem could be? Thanks.
Hi Cai,
I've moved this over to the galaxy-dev list since it pertains to a local installation.
Please make sure that the galaxy-dist/database/ directory is writable by the user running the Galaxy server. Also, if you plan to use this server for anything other than single-user development, I would suggest switching to a PostgreSQL server. This is trivial on Ubuntu (apt-get install postgresql, createuser/createdb, then edit universe_wsgi.ini as described at http://usegalaxy.org/production ).
--ndate
Best regards.
Yours: Cai ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Cai Shaojiang Department of Information Systems, School of Computing, National University of Singapore Tel: +65-65167355
On Jan 4, 2012, at 4:40 AM, Cai Shaojiang wrote:
Thanks, Nate,
I now switched to MySQL, and the problem disappeared. Thanks.
The manual highly recommend postgresql, is there any critical point to use it, instead of mysql? I am just more familiar with mysql. Thanks.
PostgreSQL support receives the most attention from the development team because it's what we use, and we've found that SQLAlchemy (the database abstraction layer used by Galaxy) seems to work better with PostgreSQL. --nate
On Wed, Jan 4, 2012 at 1:58 AM, Nate Coraor <nate@bx.psu.edu> wrote:
On Dec 29, 2011, at 12:15 AM, Cai Shaojiang wrote:
Dear friends,
We are trying to install galaxy on the server (ubuntu 11), just by following the steps on the page "Get Galaxy: Galaxy Download and Installation" of galaxy wiki. But when we start running it, it shows the following error message.
OperationalError: (OperationalError) unable to open database file u'INSERT INTO galaxy_session (create_time, update_time, user_id, remote_host, remote_addr, referer, current_history_id, session_key, is_valid, prev_session_id, disk_usage) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)' ['2011-12-29 04:52:46.575702', '2011-12-29 04:52:46.575719', None, '10.50.70.45', '10.50.70.45', None, None, '5a38b2a7e6d77a7145726cb0881eadf6', 1, None, None]
It seems something wrong with the write permission. Could you give any hint where the problem could be? Thanks.
Hi Cai,
I've moved this over to the galaxy-dev list since it pertains to a local installation.
Please make sure that the galaxy-dist/database/ directory is writable by the user running the Galaxy server. Also, if you plan to use this server for anything other than single-user development, I would suggest switching to a PostgreSQL server. This is trivial on Ubuntu (apt-get install postgresql, createuser/createdb, then edit universe_wsgi.ini as described at http://usegalaxy.org/production ).
--ndate
Best regards.
Yours: Cai ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Cai Shaojiang Department of Information Systems, School of Computing, National University of Singapore Tel: +65-65167355
The manual highly recommend postgresql, is there any critical point to use it, instead of mysql? I am just more familiar with mysql. Thanks.
The Galaxy team has found that, when running Galaxy, postgres is more stable and robust than mysql. Also, we use postgres ourselves, so it's easier for us to aid with debugging. Best, J.
OK. Thank you all. On Thu, Jan 5, 2012 at 9:32 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
The manual highly recommend postgresql, is there any critical point to use it, instead of mysql? I am just more familiar with mysql. Thanks.
The Galaxy team has found that, when running Galaxy, postgres is more stable and robust than mysql. Also, we use postgres ourselves, so it's easier for us to aid with debugging.
Best, J.
-- Cai Shaojiang Department of Information Systems, School of Computing, National University of Singapore Tel: +65-65167355
participants (3)
-
Cai Shaojiang -
Jeremy Goecks -
Nate Coraor