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.
> On Wed, Jan 4, 2012 at 1:58 AM, Nate Coraor <n...@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
>> 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 ).
>>> Best regards.
>>> Yours: Cai
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> Cai Shaojiang
> Department of Information Systems, School of Computing, National
> University of Singapore
> Tel: +65-65167355
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