Re: [galaxy-dev] Running a new installation of Galaxy on a high performance computer cluster
The database 'version' in question is our internal migration number, not the
version of your postgres install. What has happened is that since you've last
updated galaxy, the database schema has changed, and you need to kick off the
migration scripts by running 'sh manage_db.sh upgrade' in your galaxy install
directory prior to running galaxy.
-Dannon
On Sep 16, 2011, at 11:44 AM, David Matthews wrote:
> Hi,
>
> We are getting ready to run a local setup of Galaxy here at bristol
> university on our HPC cluster, BlueCrystal. We have got a mini test setup
> running fine and now we want to install it properly on the main cluster and
> have the galaxy instance run in the queue along with all the other HOC jobs
> that are submitted to BlueCrystal from around the university.
>
> The guy doing the install has just sent me this message:
>
>
>
>
> When I add the following line:
>
> database_connection = postgres://galaxy:@web1.acrc.bris.ac.uk/galaxy
>
> to
>
> universe_wsgi.ini
>
> Galaxy fails to start with the following error message:
>
> snip --
> galaxy.model.migrate.check DEBUG 2011-09-16 15:00:47,385 psycopg2 egg
> successfully loaded for postgres dialect
> Traceback (most recent call last):
> File
> "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/web/buildapp.py",
> line 82, in app_factory
> app = UniverseApplication( global_conf = global_conf, **kwargs )
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/app.py", line
> 33, in __init__
> create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
> '__file__', None ), self.config.database_engine_options )
> File
> "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py",
> line 105, in create_or_verify_database
> % ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
> Exception: Your database has version '76' but this code expects version '81'.
> Please backup your database and then migrate the schema by running 'sh
> manage_db.sh upgrade'.
>
> postgres on the web server is 8.4 so it should be fine. It looks like python
> is reporting the wrong version number.
>
> Any help from the developers would be much appreciated.
>
>
>
>
> Do you know what the problem is he is seeing? Would he be better off emailing
> you directly?
>
>
>
> Best Wishes,
> David.
>
> __
> Dr David A. Matthews
>
> Senior Lecturer in Virology
> Room E49
> Department of Cellular and Molecular Medicine,
> School of Medical Sciences
> University Walk,
> University of Bristol
> Bristol.
> BS8 1TD
> U.K.
>
> Tel. +44 117 3312058
> Fax. +44 117 3312091
>
> d.a.matth...@bristol.ac.uk
>
>
>
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
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> and other Galaxy lists, please use the interface at:
>
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Re: [galaxy-dev] Running a new installation of Galaxy on a high performance computer cluster
On Fri, Sep 16, 2011 at 4:44 PM, David Matthews
wrote:
> Hi,
> We are getting ready to run a local setup of Galaxy here at bristol
> university on our HPC cluster, BlueCrystal. We have got a mini test setup
> running fine and now we want to install it properly on the main cluster and
> have the galaxy instance run in the queue along with all the other HOC jobs
> that are submitted to BlueCrystal from around the university.
> The guy doing the install has just sent me this message:
>
>
>
> When I add the following line:
>
> database_connection = postgres://galaxy:@web1.acrc.bris.ac.uk/galaxy
>
> to
>
> universe_wsgi.ini
>
> Galaxy fails to start with the following error message:
>
> snip --
> galaxy.model.migrate.check DEBUG 2011-09-16 15:00:47,385 psycopg2 egg
> successfully loaded for postgres dialect
> Traceback (most recent call last):
> File
> "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/web/buildapp.py",
> line 82, in app_factory
> app = UniverseApplication( global_conf = global_conf, **kwargs )
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/app.py", line
> 33, in __init__
> create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
> '__file__', None ), self.config.database_engine_options )
> File
> "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py",
> line 105, in create_or_verify_database
> % ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
> Exception: Your database has version '76' but this code expects version
> '81'. Please backup your database and then migrate the schema by running
> 'sh manage_db.sh upgrade'.
>
> postgres on the web server is 8.4 so it should be fine. It looks like python
> is reporting the wrong version number.
That isn't reporting the postgres version number, but the Galaxy schema number.
> Any help from the developers would be much appreciated.
>
The error message tells you what to do,
sh manage_db.sh upgrade
>
> Do you know what the problem is he is seeing? Would he be better off
> emailing you directly?
>
This is normal when you update the Galaxy code - every so often
the Galaxy team make changes to the database tables, e.g. to add
new columns to record user disk quotas.
Peter
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[galaxy-dev] Running a new installation of Galaxy on a high performance computer cluster
Hi,
We are getting ready to run a local setup of Galaxy here at bristol university
on our HPC cluster, BlueCrystal. We have got a mini test setup running fine and
now we want to install it properly on the main cluster and have the galaxy
instance run in the queue along with all the other HOC jobs that are submitted
to BlueCrystal from around the university.
The guy doing the install has just sent me this message:
When I add the following line:
database_connection = postgres://galaxy:@web1.acrc.bris.ac.uk/galaxy
to
universe_wsgi.ini
Galaxy fails to start with the following error message:
snip --
galaxy.model.migrate.check DEBUG 2011-09-16 15:00:47,385 psycopg2 egg
successfully loaded for postgres dialect
Traceback (most recent call last):
File
"/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line
82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/app.py", line
33, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )
File
"/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py",
line 105, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '76' but this code expects version '81'.
Please backup your database and then migrate the schema by running 'sh
manage_db.sh upgrade'.
postgres on the web server is 8.4 so it should be fine. It looks like python is
reporting the wrong version number.
Any help from the developers would be much appreciated.
Do you know what the problem is he is seeing? Would he be better off emailing
you directly?
Best Wishes,
David.
__
Dr David A. Matthews
Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.
Tel. +44 117 3312058
Fax. +44 117 3312091
d.a.matth...@bristol.ac.uk
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