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.