On 24 June 2011 21:52, W. Augustine Dunn III <wadunn83@gmail.com> wrote:

Hello all:

Please forgive me if this is a matter of RTFM but I can assure you that I have in fact TRIED that for a day or so now...

I am trying to set up a local GALAXY site for my lab so that I can start to offload some of the work that comes my way as the sole biologist in our lab not afraid of the command line. My system is Ubuntu 10.10 64b, i7 quad, 12 GB RAM. Since Multiple people will be using the site I decided to go with the slightly more fancy postgresql db back-end rather than the sqlite default. I had things running fine with the sqlite but can NOT seem to get psql and galaxy to play nice.

I have created a galaxy role with rights to make tables on a created "galaxy" database:
galaxy@vlad 12:40:20 ~/galaxy-dist:

psql
psql (8.4.8)
Type "help" for help.

galaxy=> \l
List of databases

Name | Owner | Encoding | Collation | Ctype | Access privileges
--------------+----------+----------+------------+------------+-----------------------

galaxy | postgres | UTF8 | en_US.utf8 | en_US.utf8 | =Tc/postgres
: postgres=CTc/postgres

: galaxy=CTc/postgres
postgres | postgres | UTF8 | en_US.utf8 | en_US.utf8 |

template0 | postgres | UTF8 | en_US.utf8 | en_US.utf8 | =c/postgres
: postgres=CTc/postgres

template1 | postgres | UTF8 | en_US.utf8 | en_US.utf8 | =c/postgres
: postgres=CTc/postgres

zabbix_proxy | postgres | UTF8 | en_US.utf8 | en_US.utf8 |
(5 rows)

I created a PGDATA file at /var/lib/postgresql/8.4/main/PGDATA and export a PGDATA envar upon loading of the galaxy user's .bashrc pointing to this place. I am able to start and stop the server with the postgres user using pg_ctl. Once its running, I change users back to galaxy and try to run run.sh and get the following traceback:

Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory

app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 32, in __init__

create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options )

File "/home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 54, in create_or_verify_database
dataset_table = Table( "dataset", meta, autoload=True )

File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 108, in __call__
return type.__call__(self, name, metadata, *args, **kwargs)
File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 236, in __init__

_bind_or_error(metadata).reflecttable(self, include_columns=include_columns)
File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1261, in reflecttable

conn = self.contextual_connect()
File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/threadlocal.py", line 194, in contextual_connect

return self.session.get_connection(**kwargs)
File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/threadlocal.py", line 20, in get_connection

return self.engine.TLConnection(self, self.engine.pool.connect(), close_with_result=close_with_result)
File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 151, in connect

agent = _ConnectionFairy(self)
File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 304, in __init__

rec = self._connection_record = pool.get()
File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 161, in get

return self.do_get()
File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 639, in do_get

con = self.create_connection()
File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 122, in create_connection

return _ConnectionRecord(self)
File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 198, in __init__

self.connection = self.__connect()
File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 261, in __connect

connection = self.__pool._creator()
File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/strategies.py", line 80, in connect

raise exc.DBAPIError.instance(None, None, e)
OperationalError: (OperationalError) could not connect to server: No such file or directory

Is the server running locally and accepting
connections on Unix domain socket "/tmp/.s.PGSQL.5432"?

None None

I have reached the point where I am beating my head against a wall and finally decided to ask for help. I am probably not as experienced as a pure compSci person but i have been hacking python/bash/perl for years. However I am not experienced at ALL with SQL flavors.

I hope that this give someone enough info to be able to help me! Again I am sorry if this has been addressed already. I searched the archives but came up with nothing.

Thanks in advance!

Gus Dunn
Molecular Biology and Biochemistry
Institute for Genomics and Bioinformatics
Major Advisor: Anthony James
Co-Advisor: Xiaohui Xie

University of California, Irvine
2315 McGaugh Hall
Irvine, CA 92697-3900
Lab: (949) 824-3210 
Fax: (949) 824-8551
Email: dunnw@uci.edu
Email: wadunn83@gmail.com
--
In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.
-Stephen Jay Gould
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