postgresql to galaxy

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postgresql to galaxy

Hari

Hi,
      I am planning to change database from sqlite to postgresql .
      for this i installed postgresql 8.1.2 and created user and database at my home location.
      from my home i can able to login to that database
      
      psql -d galaxy -U galaxy -h 192.168.65.8
where database and user name as galaxy and hostname
I modified universal.wsgi.ini file as
database_connection =postgres:///galaxy<?user=galaxy&password=galaxy123!@#[?host=/var/run/postgresql]
database_engine_option_strategy = threadlocal
database_engine_option_server_side_cursors = True
database_engine_option_pool_size = 5
database_engine_option_max_overflow = 10

after these modification when i ran the server am getting error like this:


*****************************
Traceback (most recent call last):
File "/home/gridmon/hari/galaxy_new/galaxy-central/lib/galaxy/web/buildapp.py", line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/home/gridmon/hari/galaxy_new/galaxy-central/lib/galaxy/app.py", line 30, in __init__
create_or_verify_database( db_url, self.config.database_engine_options )
File "/home/gridmon/hari/galaxy_new/galaxy-central/lib/galaxy/model/migrate/check.py", line 54, in create_or_verify_database
dataset_table = Table( "dataset", meta, autoload=True )
File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py", line 108, in __call__
return type.__call__(self, name, metadata, *args, **kwargs)
File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py", line 236, in __init__
_bind_or_error(metadata).reflecttable(self, include_columns=include_columns)
File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1261, in reflecttable
conn = self.contextual_connect()
File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/threadlocal.py", line 194, in contextual_connect
return self.session.get_connection(**kwargs)
File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.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/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 151, in connect
agent = _ConnectionFairy(self)
File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 304, in __init__
rec = self._connection_record = pool.get()
File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 161, in get
return self.do_get()
File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 639, in do_get
con = self.create_connection()
File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 122, in create_connection
return _ConnectionRecord(self)
File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 198, in __init__
self.connection = self.__connect()
File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 261, in __connect
connection = self.__pool._creator()
File "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/strategies.py", line 80, in connect
raise exc.DBAPIError.instance(None, None, e)
OperationalError: (OperationalError) FATAL: no pg_hba.conf entry for host "[local]", user "galaxy", database "galaxy<", SSL off
*********************************************


Can any one help me for integrating postgresql to galaxy....
waiting for ur kind reply


        

--
Thanks & Regards,
Hari Krishna .M


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Re: postgresql to galaxy

Sean Davis
Hi, Hari.

You should probably make sure that you can connect to postgres from
the command line before trying to connect using galaxy.  In
particular, it looks like you need to set up this file correctly:

http://www.postgresql.org/docs/8.2/static/auth-pg-hba-conf.html

Sean


On Tue, Apr 12, 2011 at 7:50 AM, hari krishna <[hidden email]> wrote:

>
> Hi,
>       I am planning to change database from sqlite to postgresql .
>       for this i installed postgresql 8.1.2 and created user and database at
> my home location.
>       from my home i can able to login to that database
>
>
>       psql -d galaxy -U galaxy -h 192.168.65.8
>
> where database and user name as galaxy and hostname
> I modified universal.wsgi.ini file as
> database_connection
> =postgres:///galaxy<?user=galaxy&password=galaxy123!@#[?host=/var/run/postgresql]
>
> database_engine_option_strategy = threadlocal
> database_engine_option_server_side_cursors = True
> database_engine_option_pool_size = 5
>
> database_engine_option_max_overflow = 10
>
> after these modification when i ran the server am getting error like this:
>
>
> *****************************
> Traceback (most recent call last):
>
>   File
> "/home/gridmon/hari/galaxy_new/galaxy-central/lib/galaxy/web/buildapp.py",
> line 82, in app_factory
>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/home/gridmon/hari/galaxy_new/galaxy-central/lib/galaxy/app.py",
> line 30, in __init__
>
>     create_or_verify_database( db_url, self.config.database_engine_options )
>   File
> "/home/gridmon/hari/galaxy_new/galaxy-central/lib/galaxy/model/migrate/check.py",
> line 54, in create_or_verify_database
>     dataset_table = Table( "dataset", meta, autoload=True )
>
>   File
> "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py",
> line 108, in __call__
>     return type.__call__(self, name, metadata, *args, **kwargs)
>   File
> "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py",
> line 236, in __init__
>
>     _bind_or_error(metadata).reflecttable(self,
> include_columns=include_columns)
>   File
> "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py",
> line 1261, in reflecttable
>
>     conn = self.contextual_connect()
>   File
> "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/threadlocal.py",
> line 194, in contextual_connect
>     return self.session.get_connection(**kwargs)
>
>   File
> "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.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/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py",
> line 151, in connect
>     agent = _ConnectionFairy(self)
>   File
> "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py",
> line 304, in __init__
>
>     rec = self._connection_record = pool.get()
>   File
> "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py",
> line 161, in get
>     return self.do_get()
>
>   File
> "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py",
> line 639, in do_get
>     con = self.create_connection()
>   File
> "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py",
> line 122, in create_connection
>
>     return _ConnectionRecord(self)
>   File
> "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py",
> line 198, in __init__
>     self.connection = self.__connect()
>
>   File
> "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py",
> line 261, in __connect
>     connection = self.__pool._creator()
>   File
> "/home/gridmon/hari/galaxy_new/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/strategies.py",
> line 80, in connect
>
>     raise exc.DBAPIError.instance(None, None, e)
> OperationalError: (OperationalError) FATAL:  no pg_hba.conf entry for host
> "[local]", user "galaxy", database "galaxy<", SSL off
> *********************************************
>
>
>
> Can any one help me for integrating postgresql to galaxy....
> waiting for ur kind reply
>
>
>
>
> --
> Thanks & Regards,
> Hari Krishna .M
>
>

___________________________________________________________
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:

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