Have a look at https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Switching_to_a_database_server


on how to set up the PostgreSQL database for Galaxy.

I am not aware of any tools to port the contents of the SQLite file to a PostgreSQL database, except for setting up an all new Galaxy server (running with PostgreSQL) and exporting the important histories from your old server followed by importing them into your new server - though looking at the size of your history, this might not work.


Hans-Rudolf

On 03/12/2014 09:57 AM, Milad Bastami wrote:
Many thanks for your help. Your are right about database (I'm using
SQLite). I've found a tutorial at GMOD
(http://gmod.org/wiki/Galaxy_Tutorial_2012) on how to make galaxy work
with PostgreSQL, but can I change the current database to PostgreSQL
without missing my datasets? I am running a single-user galaxy instance.

Cheers, Milad


 > Date: Wed, 12 Mar 2014 09:07:00 +0100
 > From: h...@fmi.ch
 > To: mi.bast...@live.com
 > CC: galaxy-dev@lists.bx.psu.edu
 > Subject: Re: [galaxy-dev] error in workflow
 >
 > Hi Milad
 >
 > The error message: "database is locked" might be a hint.
 >
 > Are you using a PostgreSQL database or just SQLite ? If the latter, you
 > will often run in troubles when running more than one job at a time, due
 > to file locking.
 >
 > Regards, Hans-Rudolf
 >PostgreSQL
 >
 > On 03/11/2014 07:41 PM, Milad Bastami wrote:
 > > Dear Galaxy Developers,
 > > I'm running galaxy local on ubuntu and trying to run a workflow on
 > > multiple datasets (separately). Occasionally when I try to run workflow
 > > on input dataset I get "Unable to finish job" error in some steps, in
 > > most time the problem will be solved when I run the workflow again, but
 > > this going to happen more frequently. I attached the error message
here.
 > > I suspect it may be related to increase in number of datasets of the
 > > current history (1757 datasets with ~350GB size).
 > > I will appreciate your help
 > >
 > > Traceback (most recent call last):
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/runners/local.py",
line 116, in queue_job
 > > job_wrapper.finish( stdout, stderr, exit_code )
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/__init__.py",
line 1068, in finish
 > > self.sa_session.flush()
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py",
line 114, in do
 > > return getattr(self.registry(), name)(*args, **kwargs)
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
line 1718, in flush
 > > self._flush(objects)
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
line 1804, in _flush
 > > transaction.commit()
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
line 365, in commit
 > > t[1].commit()
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 2045, in commit
 > > self._do_commit()
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 2075, in _do_commit
 > > self.connection._commit_impl()
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1280, in _commit_impl
 > > self._handle_dbapi_exception(e, None, None, None, None)
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1277, in _commit_impl
 > > self.engine.dialect.do_commit(self.connection)
 > > File
"/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
line 307, in do_commit
 > > connection.commit()
 > > OperationalError: (OperationalError) database is locked None None
 > >
 > >
 > >
 > > ___________________________________________________________
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 > >
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 > > http://galaxyproject.org/search/mailinglists/
 > >
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