Hi,
Could you please show us the contents of your pg_hba.conf file? This is
where you configure which machines can access the database through the
network.
Best,
L-A
Le 27/06/2011 20:33, Marco Moretto a écrit :
Hi Gus,
it seems that your postgres is not configured to accept connection
except localhost (or the deamon is not running). Did you try to
connect to postgres from another PC in the network (no the localhost)?
Did you install postgres using apt-get install? Do you run postgres
using "/etc/init.d/postgresql-8.4 start"?
Greets.
---
Marco
On 24 June 2011 21:52, W. Augustine Dunn III <[email protected]
<mailto:[email protected]>> 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:[email protected] <mailto:[email protected]>
Email:[email protected] <mailto:[email protected]>
--
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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