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: du...@uci.edu
Email: wadun...@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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