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 <wadun...@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: 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*
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to