Error in installing Galaxy.

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Error in installing Galaxy.

sridhar srinivasan

Hi ,

I am getting error during Installing galaxy locally.

Traceback (most recent call last):
  File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/app.py", line 51, in __init__
    create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self )
  File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 50, in create_or_verify_database
    dataset_table = Table( "dataset", meta, autoload=True )
  File "/illumina/apps/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 "/illumina/apps/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 "/illumina/apps/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 "/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1229, in contextual_connect
    return self.Connection(self, self.pool.connect(), close_with_result=close_with_result, **kwargs)
  File "/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 142, in connect
    return _ConnectionFairy(self).checkout()
  File "/illumina/apps/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 "/illumina/apps/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 "/illumina/apps/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 "/illumina/apps/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 "/illumina/apps/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 "/illumina/apps/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 "/illumina/apps/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) FATAL:  Ident authentication failed for user "galaxy"
 None None

I created a user galaxy to install galaxy locally.

Thanks in Advance.

Sridhar


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Re: Error in installing Galaxy.

Hans-Rudolf Hotz
Hi Sridhar

Have you set up your PostgreSQL database correctly? and provide the
right  username and password in the 'universe_wsgi.ini' file ?

See:
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerformance#Switching_to_a_database_server

Also, see this old thread, where the same error has been reported before:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002624.html



Regards, Hans-Rudolf



On 05/08/2013 01:24 PM, sridhar srinivasan wrote:

>
> Hi ,
>
> I am getting error during Installing galaxy locally.
>
> Traceback (most recent call last):
>    File
> "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
> line 35, in app_factory
>      app = UniverseApplication( global_conf = global_conf, **kwargs )
>    File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/app.py", line 51,
> in __init__
>      create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
> ).get( '__file__', None ), self.config.database_engine_options, app=self )
>    File
> "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py",
> line 50, in create_or_verify_database
>      dataset_table = Table( "dataset", meta, autoload=True )
>    File
> "/illumina/apps/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
> "/illumina/apps/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
> "/illumina/apps/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
> "/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 1229, in contextual_connect
>      return self.Connection(self, self.pool.connect(),
> close_with_result=close_with_result, **kwargs)
>    File
> "/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
> line 142, in connect
>      return _ConnectionFairy(self).checkout()
>    File
> "/illumina/apps/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
> "/illumina/apps/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
> "/illumina/apps/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
> "/illumina/apps/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
> "/illumina/apps/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
> "/illumina/apps/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
> "/illumina/apps/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) FATAL:  Ident authentication failed
> for user "galaxy"
>   None None
>
> I created a user galaxy to install galaxy locally.
>
> Thanks in Advance.
>
> Sridhar
>
>
>
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>
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Re: Error in installing Galaxy.

sridhar srinivasan
Hi Rudolf,

Thanks for the reply.

Previously i was using the
postgres://user:pass@host/galaxy  in 'universe_wsgi.ini' 

now i tried with 
postgres:///<db_name><?user=user_name&password=your_pass>

and it is working.. but i could'nt connect to the webpage http://127.0.0.1:8080/ from another system in same network..

Sridhar


On Wed, May 8, 2013 at 7:16 PM, Hans-Rudolf Hotz <[hidden email]> wrote:
Hi Sridhar

Have you set up your PostgreSQL database correctly? and provide the right  username and password in the 'universe_wsgi.ini' file ?

See: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerformance#Switching_to_a_database_server

Also, see this old thread, where the same error has been reported before:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002624.html



Regards, Hans-Rudolf




On 05/08/2013 01:24 PM, sridhar srinivasan wrote:

Hi ,

I am getting error during Installing galaxy locally.

Traceback (most recent call last):
   File
"/illumina/apps/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
line 35, in app_factory
     app = UniverseApplication( global_conf = global_conf, **kwargs )
   File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/app.py", line 51,
in __init__
     create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
).get( '__file__', None ), self.config.database_engine_options, app=self )
   File
"/illumina/apps/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py",
line 50, in create_or_verify_database
     dataset_table = Table( "dataset", meta, autoload=True )
   File
"/illumina/apps/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
"/illumina/apps/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
"/illumina/apps/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
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
line 1229, in contextual_connect
     return self.Connection(self, self.pool.connect(),
close_with_result=close_with_result, **kwargs)
   File
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 142, in connect
     return _ConnectionFairy(self).checkout()
   File
"/illumina/apps/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
"/illumina/apps/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
"/illumina/apps/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
"/illumina/apps/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
"/illumina/apps/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
"/illumina/apps/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
"/illumina/apps/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) FATAL:  Ident authentication failed
for user "galaxy"
  None None

I created a user galaxy to install galaxy locally.

Thanks in Advance.

Sridhar



___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

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   http://galaxyproject.org/search/mailinglists/



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Re: Error in installing Galaxy.

Dannon Baker-2
On Thu, May 9, 2013 at 12:21 AM, sridhar srinivasan <[hidden email]> wrote:
and it is working.. but i could'nt connect to the webpage http://127.0.0.1:8080/ from another system in same network..

By default, galaxy will only be serving on 127.0.0.1 (localhost), which is a loopback and only accessible on the machine itself.  Accessing 127.0.0.1 using another machine on the network is actually making requests to the machine you're trying that from, which I assume isn't running galaxy.

In your universe_wsgi.ini, you can edit this via the 'host' setting.  Just use 0.0.0.0 to listen to all connections.

-Dannon

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Re: Error in installing Galaxy.

sridhar srinivasan
Thanks for the reply..
Yeah i am using the Host=0.0.0.0 but i couldn't connect..

now after installing ngnix and reloading i am getting error like..

Traceback (most recent call last):
  File "./scripts/paster.py", line 33, in <module>
    serve.run()
  File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1056, in run
    invoke(command, command_name, options, args[1:])
  File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1062, in invoke
    exit_code = runner.run(args)
  File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 227, in run
    result = self.command()
  File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 677, in command
    serve()
  File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 661, in serve
    server(app)
  File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 292, in server_wrapper
    **context.local_conf)
  File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call
    val = callable(*args, **kw)
  File "/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1342, in server_runner
    serve(wsgi_app, **kwargs)
  File "/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1291, in serve
    request_queue_size=request_queue_size)
  File "/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1134, in __init__
    request_queue_size=request_queue_size)
  File "/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1113, in __init__
    request_queue_size=request_queue_size)
  File "/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 328, in __init__
    HTTPServer.__init__(self, server_address, RequestHandlerClass)
  File "/usr/lib64/python2.6/SocketServer.py", line 402, in __init__
    self.server_bind()
  File "/usr/lib64/python2.6/BaseHTTPServer.py", line 108, in server_bind
    SocketServer.TCPServer.server_bind(self)
  File "/usr/lib64/python2.6/SocketServer.py", line 413, in server_bind
    self.socket.bind(self.server_address)
  File "<string>", line 1, in bind
socket.error: [Errno 98] Address already in use
galaxy.jobs.handler INFO 2013-05-10 10:22:14,360 sending stop signal to worker thread
galaxy.jobs.handler INFO 2013-05-10 10:22:14,360 job handler queue stopped
galaxy.jobs.runners INFO 2013-05-10 10:22:14,360 LWRRunner: Sending stop signal to monitor thread
galaxy.jobs.runners INFO 2013-05-10 10:22:14,360 LWRRunner: Sending stop signal to 3 worker threads
galaxy.jobs.runners INFO 2013-05-10 10:22:14,360 LocalRunner: Sending stop signal to 5 worker threads
galaxy.jobs.handler INFO 2013-05-10 10:22:14,362 sending stop signal to worker thread
galaxy.jobs.handler INFO 2013-05-10 10:22:14,362 job handler stop queue stopped
Exception in thread LWRRunner.monitor_thread (most likely raised during interpreter shutdown):Exception in thread JobHandlerQueue.monitor_thread (most likely raised during interpreter shutdown):

Traceback (most recent call last):
Traceback (most recent call last):




On Thu, May 9, 2013 at 5:15 PM, Dannon Baker <[hidden email]> wrote:
On Thu, May 9, 2013 at 12:21 AM, sridhar srinivasan <[hidden email]> wrote:
and it is working.. but i could'nt connect to the webpage http://127.0.0.1:8080/ from another system in same network..

By default, galaxy will only be serving on 127.0.0.1 (localhost), which is a loopback and only accessible on the machine itself.  Accessing 127.0.0.1 using another machine on the network is actually making requests to the machine you're trying that from, which I assume isn't running galaxy.

In your universe_wsgi.ini, you can edit this via the 'host' setting.  Just use 0.0.0.0 to listen to all connections.

-Dannon


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Re: Error in installing Galaxy.

sridhar srinivasan
In reply to this post by Hans-Rudolf Hotz
Hi Rudolf,
Thanks for the reply..

Could you please tell how to check and set the PostgreSQL ..
I provide the correct username and password in universe.ini file..

when i give

#database_connection = postgres:///galaxy_prod ?user=galaxy&password=password
it gave error in history page
"""
Content Encoding Error


The page you are trying to view cannot be shown because it uses an invalid or unsupported form of compression.

    *   Please contact the website owners to inform them of this problem.

"""


Now after changing it into

database_connection = postgres://galaxy:password@localhost:5432/galaxy_prod

it gives error which i mentioned in previous mail....

Please suggest on this

Thanks
Sridhar


On Wed, May 8, 2013 at 7:16 PM, Hans-Rudolf Hotz <[hidden email]> wrote:
Hi Sridhar

Have you set up your PostgreSQL database correctly? and provide the right  username and password in the 'universe_wsgi.ini' file ?

See: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerformance#Switching_to_a_database_server

Also, see this old thread, where the same error has been reported before:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002624.html



Regards, Hans-Rudolf




On 05/08/2013 01:24 PM, sridhar srinivasan wrote:

Hi ,

I am getting error during Installing galaxy locally.

Traceback (most recent call last):
   File
"/illumina/apps/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
line 35, in app_factory
     app = UniverseApplication( global_conf = global_conf, **kwargs )
   File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/app.py", line 51,
in __init__
     create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
).get( '__file__', None ), self.config.database_engine_options, app=self )
   File
"/illumina/apps/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py",
line 50, in create_or_verify_database
     dataset_table = Table( "dataset", meta, autoload=True )
   File
"/illumina/apps/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
"/illumina/apps/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
"/illumina/apps/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
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
line 1229, in contextual_connect
     return self.Connection(self, self.pool.connect(),
close_with_result=close_with_result, **kwargs)
   File
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 142, in connect
     return _ConnectionFairy(self).checkout()
   File
"/illumina/apps/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
"/illumina/apps/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
"/illumina/apps/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
"/illumina/apps/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
"/illumina/apps/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
"/illumina/apps/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
"/illumina/apps/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) FATAL:  Ident authentication failed
for user "galaxy"
  None None

I created a user galaxy to install galaxy locally.

Thanks in Advance.

Sridhar



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Re: Error in installing Galaxy.

Hans-Rudolf Hotz


On 05/21/2013 11:22 AM, sridhar srinivasan wrote:

> Hi Rudolf,
> Thanks for the reply..
>
> Could you please tell how to check and set the PostgreSQL ..
> I provide the correct username and password in universe.ini file..
>
> when i give
>
> #database_connection = postgres:///galaxy_prod
> ?user=galaxy&password=password
> it gave error in history page
> """
> Content Encoding Error
>
>
> The page you are trying to view cannot be shown because it uses an
> invalid or unsupported form of compression.
>
>      *   Please contact the website owners to inform them of this problem.
>
> """
>
>
> Now after changing it into
>
> database_connection = postgres://galaxy:password@localhost:5432/galaxy_prod
>
> it gives error which i mentioned in previous mail....
>
> Please suggest on this


Assuming you replace 'password' with the actual password, the line looks
correct to me. Try replacing 'localhost' with the IP address


Regards, Hans-Rudolf



>
> Thanks
> Sridhar
>
>
> On Wed, May 8, 2013 at 7:16 PM, Hans-Rudolf Hotz <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi Sridhar
>
>     Have you set up your PostgreSQL database correctly? and provide the
>     right  username and password in the 'universe_wsgi.ini' file ?
>
>     See:
>     <a href="http://wiki.galaxyproject.org/__Admin/Config/Performance/__ProductionServer?action=show&__redirect=Admin%2FConfig%__2FPerformance#Switching_to_a___database_server">http://wiki.galaxyproject.org/__Admin/Config/Performance/__ProductionServer?action=show&__redirect=Admin%2FConfig%__2FPerformance#Switching_to_a___database_server
>     <http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerformance#Switching_to_a_database_server>
>
>     Also, see this old thread, where the same error has been reported
>     before:
>     http://lists.bx.psu.edu/__pipermail/galaxy-dev/2010-May/__002624.html <http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002624.html>
>
>
>
>     Regards, Hans-Rudolf
>
>
>
>
>     On 05/08/2013 01:24 PM, sridhar srinivasan wrote:
>
>
>         Hi ,
>
>         I am getting error during Installing galaxy locally.
>
>         Traceback (most recent call last):
>             File
>         "/illumina/apps/galaxy/galaxy-__dist/lib/galaxy/webapps/__galaxy/buildapp.py",
>         line 35, in app_factory
>               app = UniverseApplication( global_conf = global_conf,
>         **kwargs )
>             File
>         "/illumina/apps/galaxy/galaxy-__dist/lib/galaxy/app.py", line 51,
>         in __init__
>               create_or_verify_database( db_url, kwargs.get(
>         'global_conf', {}
>         ).get( '__file__', None ),
>         self.config.database_engine___options, app=self )
>             File
>         "/illumina/apps/galaxy/galaxy-__dist/lib/galaxy/model/migrate/__check.py",
>         line 50, in create_or_verify_database
>               dataset_table = Table( "dataset", meta, autoload=True )
>             File
>         "/illumina/apps/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
>         "/illumina/apps/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
>         "/illumina/apps/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
>         "/illumina/apps/galaxy/galaxy-__dist/eggs/SQLAlchemy-0.5.6___dev_r6498-py2.6.egg/__sqlalchemy/engine/base.py",
>         line 1229, in contextual_connect
>               return self.Connection(self, self.pool.connect(),
>         close_with_result=close_with___result, **kwargs)
>             File
>         "/illumina/apps/galaxy/galaxy-__dist/eggs/SQLAlchemy-0.5.6___dev_r6498-py2.6.egg/__sqlalchemy/pool.py",
>         line 142, in connect
>               return _ConnectionFairy(self).__checkout()
>             File
>         "/illumina/apps/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
>         "/illumina/apps/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
>         "/illumina/apps/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
>         "/illumina/apps/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
>         "/illumina/apps/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
>         "/illumina/apps/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
>         "/illumina/apps/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) FATAL:  Ident
>         authentication failed
>         for user "galaxy"
>            None None
>
>         I created a user galaxy to install galaxy locally.
>
>         Thanks in Advance.
>
>         Sridhar
>
>
>
>         _____________________________________________________________
>         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/
>
>         To search Galaxy mailing lists use the unified search at:
>         http://galaxyproject.org/__search/mailinglists/
>         <http://galaxyproject.org/search/mailinglists/>
>
>
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Re: Error in installing Galaxy.

sridhar srinivasan
Hello Rudolf,
I tried with the IP address it gave the error as
"""
Is the server running on host "192.168.1.1" and accepting
        TCP/IP connections on port 5432?
"""
Then i try with 0.0.0.0 again i got same error

OperationalError: (OperationalError) FATAL:  Ident authentication failed for user "galaxy"
 None None

Thanks
Sridhar


On Tue, May 21, 2013 at 3:08 PM, Hans-Rudolf Hotz <[hidden email]> wrote:


On 05/21/2013 11:22 AM, sridhar srinivasan wrote:
Hi Rudolf,
Thanks for the reply..

Could you please tell how to check and set the PostgreSQL ..
I provide the correct username and password in universe.ini file..

when i give

#database_connection = postgres:///galaxy_prod
?user=galaxy&password=password
it gave error in history page
"""
Content Encoding Error


The page you are trying to view cannot be shown because it uses an
invalid or unsupported form of compression.

     *   Please contact the website owners to inform them of this problem.

"""


Now after changing it into

database_connection = postgres://galaxy:password@localhost:5432/galaxy_prod

it gives error which i mentioned in previous mail....

Please suggest on this


Assuming you replace 'password' with the actual password, the line looks correct to me. Try replacing 'localhost' with the IP address


Regards, Hans-Rudolf




Thanks
Sridhar


On Wed, May 8, 2013 at 7:16 PM, Hans-Rudolf Hotz <[hidden email]
<mailto:[hidden email]>> wrote:

    Hi Sridhar

    Have you set up your PostgreSQL database correctly? and provide the
    right  username and password in the 'universe_wsgi.ini' file ?

    See:
    <a href="http://wiki.galaxyproject.org/__Admin/Config/Performance/__ProductionServer?action=show&amp;__redirect=Admin%2FConfig%__2FPerformance#Switching_to_a___database_server" target="_blank">http://wiki.galaxyproject.org/__Admin/Config/Performance/__ProductionServer?action=show&__redirect=Admin%2FConfig%__2FPerformance#Switching_to_a___database_server     http://lists.bx.psu.edu/__pipermail/galaxy-dev/2010-May/__002624.html <http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002624.html>




    Regards, Hans-Rudolf




    On 05/08/2013 01:24 PM, sridhar srinivasan wrote:


        Hi ,

        I am getting error during Installing galaxy locally.

        Traceback (most recent call last):
            File
        "/illumina/apps/galaxy/galaxy-__dist/lib/galaxy/webapps/__galaxy/buildapp.py",

        line 35, in app_factory
              app = UniverseApplication( global_conf = global_conf,
        **kwargs )
            File
        "/illumina/apps/galaxy/galaxy-__dist/lib/galaxy/app.py", line 51,

        in __init__
              create_or_verify_database( db_url, kwargs.get(
        'global_conf', {}
        ).get( '__file__', None ),
        self.config.database_engine___options, app=self )
            File
        "/illumina/apps/galaxy/galaxy-__dist/lib/galaxy/model/migrate/__check.py",

        line 50, in create_or_verify_database
              dataset_table = Table( "dataset", meta, autoload=True )
            File
        "/illumina/apps/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
        "/illumina/apps/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
        "/illumina/apps/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
        "/illumina/apps/galaxy/galaxy-__dist/eggs/SQLAlchemy-0.5.6___dev_r6498-py2.6.egg/__sqlalchemy/engine/base.py",

        line 1229, in contextual_connect
              return self.Connection(self, self.pool.connect(),
        close_with_result=close_with___result, **kwargs)
            File
        "/illumina/apps/galaxy/galaxy-__dist/eggs/SQLAlchemy-0.5.6___dev_r6498-py2.6.egg/__sqlalchemy/pool.py",
        line 142, in connect
              return _ConnectionFairy(self).__checkout()
            File
        "/illumina/apps/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
        "/illumina/apps/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
        "/illumina/apps/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
        "/illumina/apps/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
        "/illumina/apps/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
        "/illumina/apps/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
        "/illumina/apps/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) FATAL:  Ident
        authentication failed
        for user "galaxy"
           None None

        I created a user galaxy to install galaxy locally.

        Thanks in Advance.

        Sridhar



        _____________________________________________________________

        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/

        To search Galaxy mailing lists use the unified search at:
        http://galaxyproject.org/__search/mailinglists/
        <http://galaxyproject.org/search/mailinglists/>




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Re: Error in installing Galaxy.

Hans-Rudolf Hotz
Hi Sridhar

Since we are using MySQL for our Galaxy server, I am kind of running out
of ideas...and hope someone else on the list can spot the error in your
universe.ini file.

Just one last remark to double check:

Can you log into the PostgreSQL database with the same credentials from
the command line?

psql -d galaxy_prod -p 5432 -h localhost -U galaxy

and this should prompt for the password
(again, I am not an PostgreSQL expert...)


Regards, Hans-Rudolf



On 05/21/2013 01:00 PM, sridhar srinivasan wrote:

> Hello Rudolf,
> I tried with the IP address it gave the error as
> """
> Is the server running on host "192.168.1.1" and accepting
>          TCP/IP connections on port 5432?
> """
> Then i try with 0.0.0.0 again i got same error
>
> OperationalError: (OperationalError) FATAL:  Ident authentication failed
> for user "galaxy"
>   None None
>
> Thanks
> Sridhar
>
>
> On Tue, May 21, 2013 at 3:08 PM, Hans-Rudolf Hotz <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>
>
>     On 05/21/2013 11:22 AM, sridhar srinivasan wrote:
>
>         Hi Rudolf,
>         Thanks for the reply..
>
>         Could you please tell how to check and set the PostgreSQL ..
>         I provide the correct username and password in universe.ini file..
>
>         when i give
>
>         #database_connection = postgres:///galaxy_prod
>         ?user=galaxy&password=password
>         it gave error in history page
>         """
>         Content Encoding Error
>
>
>         The page you are trying to view cannot be shown because it uses an
>         invalid or unsupported form of compression.
>
>               *   Please contact the website owners to inform them of
>         this problem.
>
>         """
>
>
>         Now after changing it into
>
>         database_connection =
>         postgres://galaxy:password@__localhost:5432/galaxy_prod
>
>         it gives error which i mentioned in previous mail....
>
>         Please suggest on this
>
>
>
>     Assuming you replace 'password' with the actual password, the line
>     looks correct to me. Try replacing 'localhost' with the IP address
>
>
>     Regards, Hans-Rudolf
>
>
>
>
>         Thanks
>         Sridhar
>
>
>         On Wed, May 8, 2013 at 7:16 PM, Hans-Rudolf Hotz <[hidden email]
>         <mailto:[hidden email]>
>         <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
>
>              Hi Sridhar
>
>              Have you set up your PostgreSQL database correctly? and
>         provide the
>              right  username and password in the 'universe_wsgi.ini' file ?
>
>              See:
>         <a href="http://wiki.galaxyproject.org/____Admin/Config/Performance/____ProductionServer?action=show&____redirect=Admin%2FConfig%____2FPerformance#Switching_to_a_____database_server">http://wiki.galaxyproject.org/____Admin/Config/Performance/____ProductionServer?action=show&____redirect=Admin%2FConfig%____2FPerformance#Switching_to_a_____database_server
>         <<a href="http://wiki.galaxyproject.org/__Admin/Config/Performance/__ProductionServer?action=show&__redirect=Admin%2FConfig%__2FPerformance#Switching_to_a___database_server">http://wiki.galaxyproject.org/__Admin/Config/Performance/__ProductionServer?action=show&__redirect=Admin%2FConfig%__2FPerformance#Switching_to_a___database_server>
>
>
>         <<a href="http://wiki.galaxyproject.__org/Admin/Config/Performance/__ProductionServer?action=show&__redirect=Admin%2FConfig%__2FPerformance#Switching_to_a___database_server">http://wiki.galaxyproject.__org/Admin/Config/Performance/__ProductionServer?action=show&__redirect=Admin%2FConfig%__2FPerformance#Switching_to_a___database_server
>         <http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerformance#Switching_to_a_database_server>>
>
>              Also, see this old thread, where the same error has been
>         reported
>              before:
>         http://lists.bx.psu.edu/____pipermail/galaxy-dev/2010-May/____002624.html
>         <http://lists.bx.psu.edu/__pipermail/galaxy-dev/2010-May/__002624.html>
>         <http://lists.bx.psu.edu/__pipermail/galaxy-dev/2010-May/__002624.html
>         <http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002624.html>>
>
>
>
>
>              Regards, Hans-Rudolf
>
>
>
>
>              On 05/08/2013 01:24 PM, sridhar srinivasan wrote:
>
>
>                  Hi ,
>
>                  I am getting error during Installing galaxy locally.
>
>                  Traceback (most recent call last):
>                      File
>
>         "/illumina/apps/galaxy/galaxy-____dist/lib/galaxy/webapps/____galaxy/buildapp.py",
>
>                  line 35, in app_factory
>                        app = UniverseApplication( global_conf = global_conf,
>                  **kwargs )
>                      File
>
>         "/illumina/apps/galaxy/galaxy-____dist/lib/galaxy/app.py", line 51,
>
>                  in __init__
>                        create_or_verify_database( db_url, kwargs.get(
>                  'global_conf', {}
>                  ).get( '__file__', None ),
>                  self.config.database_engine_____options, app=self )
>                      File
>
>         "/illumina/apps/galaxy/galaxy-____dist/lib/galaxy/model/__migrate/__check.py",
>
>                  line 50, in create_or_verify_database
>                        dataset_table = Table( "dataset", meta,
>         autoload=True )
>                      File
>
>         "/illumina/apps/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
>
>         "/illumina/apps/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
>
>         "/illumina/apps/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
>
>         "/illumina/apps/galaxy/galaxy-____dist/eggs/SQLAlchemy-0.5.6_____dev_r6498-py2.6.egg/____sqlalchemy/engine/base.py",
>
>                  line 1229, in contextual_connect
>                        return self.Connection(self, self.pool.connect(),
>                  close_with_result=close_with_____result, **kwargs)
>                      File
>
>         "/illumina/apps/galaxy/galaxy-____dist/eggs/SQLAlchemy-0.5.6_____dev_r6498-py2.6.egg/____sqlalchemy/pool.py",
>                  line 142, in connect
>                        return _ConnectionFairy(self).____checkout()
>                      File
>
>         "/illumina/apps/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
>
>         "/illumina/apps/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
>
>         "/illumina/apps/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
>
>         "/illumina/apps/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
>
>         "/illumina/apps/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
>
>         "/illumina/apps/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
>
>         "/illumina/apps/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) FATAL:  Ident
>                  authentication failed
>                  for user "galaxy"
>                     None None
>
>                  I created a user galaxy to install galaxy locally.
>
>                  Thanks in Advance.
>
>                  Sridhar
>
>
>
>
>         _________________________________________________________________
>
>                  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/
>
>                  To search Galaxy mailing lists use the unified search at:
>         http://galaxyproject.org/____search/mailinglists/
>         <http://galaxyproject.org/__search/mailinglists/>
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>
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Re: Error in installing Galaxy.

sridhar srinivasan
Hello Rudolf,
Thanks for the reply..

I use the command you mentioned in reply..
and the error is "psql: FATAL:  Ident authentication failed for user "galaxy" "

Thanks
Sridhar


On Tue, May 21, 2013 at 4:53 PM, Hans-Rudolf Hotz <[hidden email]> wrote:
Hi Sridhar

Since we are using MySQL for our Galaxy server, I am kind of running out of ideas...and hope someone else on the list can spot the error in your universe.ini file.

Just one last remark to double check:

Can you log into the PostgreSQL database with the same credentials from the command line?

psql -d galaxy_prod -p 5432 -h localhost -U galaxy

and this should prompt for the password
(again, I am not an PostgreSQL expert...)


Regards, Hans-Rudolf




On 05/21/2013 01:00 PM, sridhar srinivasan wrote:
Hello Rudolf,
I tried with the IP address it gave the error as
"""
Is the server running on host "192.168.1.1" and accepting
         TCP/IP connections on port 5432?
"""
Then i try with 0.0.0.0 again i got same error

OperationalError: (OperationalError) FATAL:  Ident authentication failed
for user "galaxy"
  None None

Thanks
Sridhar


On Tue, May 21, 2013 at 3:08 PM, Hans-Rudolf Hotz <[hidden email]
<mailto:[hidden email]>> wrote:



    On 05/21/2013 11:22 AM, sridhar srinivasan wrote:

        Hi Rudolf,
        Thanks for the reply..

        Could you please tell how to check and set the PostgreSQL ..
        I provide the correct username and password in universe.ini file..

        when i give

        #database_connection = postgres:///galaxy_prod
        ?user=galaxy&password=password
        it gave error in history page
        """
        Content Encoding Error


        The page you are trying to view cannot be shown because it uses an
        invalid or unsupported form of compression.

              *   Please contact the website owners to inform them of
        this problem.

        """


        Now after changing it into

        database_connection =
        postgres://galaxy:password@__localhost:5432/galaxy_prod


        it gives error which i mentioned in previous mail....

        Please suggest on this



    Assuming you replace 'password' with the actual password, the line
    looks correct to me. Try replacing 'localhost' with the IP address


    Regards, Hans-Rudolf




        Thanks
        Sridhar


        On Wed, May 8, 2013 at 7:16 PM, Hans-Rudolf Hotz <[hidden email]
        <mailto:[hidden email]>
        <mailto:[hidden email] <mailto:[hidden email]>>> wrote:

             Hi Sridhar

             Have you set up your PostgreSQL database correctly? and
        provide the
             right  username and password in the 'universe_wsgi.ini' file ?

             See:
        <a href="http://wiki.galaxyproject.org/____Admin/Config/Performance/____ProductionServer?action=show&amp;____redirect=Admin%2FConfig%____2FPerformance#Switching_to_a_____database_server" target="_blank">http://wiki.galaxyproject.org/____Admin/Config/Performance/____ProductionServer?action=show&____redirect=Admin%2FConfig%____2FPerformance#Switching_to_a_____database_server
        <<a href="http://wiki.galaxyproject.org/__Admin/Config/Performance/__ProductionServer?action=show&amp;__redirect=Admin%2FConfig%__2FPerformance#Switching_to_a___database_server" target="_blank">http://wiki.galaxyproject.org/__Admin/Config/Performance/__ProductionServer?action=show&__redirect=Admin%2FConfig%__2FPerformance#Switching_to_a___database_server>


        <http://wiki.galaxyproject.__org/Admin/Config/Performance/__ProductionServer?action=show&__redirect=Admin%2FConfig%__2FPerformance#Switching_to_a___database_server

        <http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerformance#Switching_to_a_database_server>>

             Also, see this old thread, where the same error has been
        reported
             before:
        http://lists.bx.psu.edu/____pipermail/galaxy-dev/2010-May/____002624.html
        <http://lists.bx.psu.edu/__pipermail/galaxy-dev/2010-May/__002624.html>

        <http://lists.bx.psu.edu/__pipermail/galaxy-dev/2010-May/__002624.html
        <http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002624.html>>




             Regards, Hans-Rudolf




             On 05/08/2013 01:24 PM, sridhar srinivasan wrote:


                 Hi ,

                 I am getting error during Installing galaxy locally.

                 Traceback (most recent call last):
                     File

        "/illumina/apps/galaxy/galaxy-____dist/lib/galaxy/webapps/____galaxy/buildapp.py",


                 line 35, in app_factory
                       app = UniverseApplication( global_conf = global_conf,
                 **kwargs )
                     File

        "/illumina/apps/galaxy/galaxy-____dist/lib/galaxy/app.py", line 51,


                 in __init__
                       create_or_verify_database( db_url, kwargs.get(
                 'global_conf', {}
                 ).get( '__file__', None ),
                 self.config.database_engine_____options, app=self )
                     File

        "/illumina/apps/galaxy/galaxy-____dist/lib/galaxy/model/__migrate/__check.py",


                 line 50, in create_or_verify_database
                       dataset_table = Table( "dataset", meta,
        autoload=True )
                     File

        "/illumina/apps/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

        "/illumina/apps/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

        "/illumina/apps/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

        "/illumina/apps/galaxy/galaxy-____dist/eggs/SQLAlchemy-0.5.6_____dev_r6498-py2.6.egg/____sqlalchemy/engine/base.py",


                 line 1229, in contextual_connect
                       return self.Connection(self, self.pool.connect(),
                 close_with_result=close_with_____result, **kwargs)
                     File

        "/illumina/apps/galaxy/galaxy-____dist/eggs/SQLAlchemy-0.5.6_____dev_r6498-py2.6.egg/____sqlalchemy/pool.py",
                 line 142, in connect
                       return _ConnectionFairy(self).____checkout()
                     File

        "/illumina/apps/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

        "/illumina/apps/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

        "/illumina/apps/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

        "/illumina/apps/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

        "/illumina/apps/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

        "/illumina/apps/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

        "/illumina/apps/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) FATAL:  Ident
                 authentication failed
                 for user "galaxy"
                    None None

                 I created a user galaxy to install galaxy locally.

                 Thanks in Advance.

                 Sridhar




        _________________________________________________________________


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Re: Error in installing Galaxy.

James Taylor
On Tue, May 21, 2013 at 7:36 AM, sridhar srinivasan
<[hidden email]> wrote:
> I use the command you mentioned in reply..
> and the error is "psql: FATAL:  Ident authentication failed for user
> "galaxy" "

Your problem is then not in Galaxy. Your postgresql server either does
not have a galaxy user or does not allow ident authentication for that
user.

--
James Taylor, Assistant Professor, Biology/CS, Emory University
___________________________________________________________
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