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 <wadun...@gmail.com <mailto: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  <mailto:du...@uci.edu>
    Email:wadun...@gmail.com  <mailto: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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