Hi Peter,

I know that ;)  Still I am curious about the possible solution. Any ideas?

Regards,

Pieter.

From: Peter Cock [mailto:p.j.a.cock@googlemail.com]
Sent: woensdag 18 december 2013 13:31
To: Lukasse, Pieter
Cc: Galaxy Dev
Subject: Re: New Galaxy won't start, SQLite (OperationalError) database is locked

Hi Pieter,

Using SQLite is NOT recommended for a production Galaxy,

it is only really used for development and testing (having the

whole database as one file on disk without worrying about

creating a proper database, user accounts etc is nice).

Peter

On Wednesday, December 18, 2013, Lukasse, Pieter wrote:

Hi Peter,

Thanks for reporting this. I am now facing the same error, but I don't get it....  For example: normally it appears when I try to change something in the DB (e.g. adding a new history), but then suddenly I managed to create one new history item....and now it is occurring again. It seems to be a transient locked state, so every now and then the lock is released somehow.

Anyway, are there any ideas on what could be a real solution to this problem? This is the second Galaxy server I upgrade which now is stuck after the upgrade...any help is appreciated!

Thanks and regards,

Pieter.

-----Original Message-----
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Peter Cock
Sent: donderdag 31 oktober 2013 11:54
To: Galaxy Dev
Subject: [galaxy-dev] New Galaxy won't start, SQLite (OperationalError) database is locked

Hello all,

While attempting a fresh Galaxy install from both galaxy-central and galaxy-dist, I ran into a problem initialising the default SQLite database (database/universe.sqlite),

$ hg clone https://bitbucket.org/galaxy/galaxy-dist
...
$ cd galaxy-dist
$ ./run.sh
...
galaxy.model.migrate.check DEBUG 2013-10-31 10:28:26,143 pysqlite>=2 egg successfully loaded for sqlite dialect Traceback (most recent call last):
...
OperationalError: (OperationalError) database is locked u'PRAGMA table_info("dataset")' ()

After some puzzlement, I realised this was down to the file system - I was trying this under my home directory mounted via a distributed file system (gluster I think).

Repeating the experiment under /tmp on a local hard disk worked :)

(I'm posting this message for future reference; hopefully Google and/or mailing list searches will help anyone else facing this error)

Regards,

Peter
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