Re: [galaxy-dev] Error in installing Galaxy.

2013-05-21 Thread James Taylor 
On Tue, May 21, 2013 at 7:36 AM, sridhar srinivasan
 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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Re: [galaxy-dev] Error in installing Galaxy.

2013-05-21 Thread 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  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 > > 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 > 
>> >> 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
>> > *ProductionServer?action=show&_**_redirect=Admin%2FConfig%__**
>> 2FPerformance#Switching_to_a__**_database_server>
>>
>>
>> > _ProductionServer?action=show&**__redirect=Admin%2FConfig%__**
>> 2FPerformance#Switching_to_a__**_database_server
>>
>> > 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
>> > __002624.html
>> >
>>
>> > __002624.html
>> > 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-**d

Re: [galaxy-dev] Error in installing Galaxy.

2013-05-21 Thread 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 mailto:h...@fmi.ch>> 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 mailto:h...@fmi.ch>
>> 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/g

Re: [galaxy-dev] Error in installing Galaxy.

2013-05-21 Thread 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  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 > > 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
>>
>> > 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
>>

Re: [galaxy-dev] Error in installing Galaxy.

2013-05-21 Thread 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 mailto:h...@fmi.ch>> 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/egg

Re: [galaxy-dev] Error in installing Galaxy.

2013-05-21 Thread sridhar srinivasan 
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  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
>>
>>
>>

Re: [galaxy-dev] Error in installing Galaxy.

2013-05-09 Thread 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 
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 "", 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  wrote:

> On Thu, May 9, 2013 at 12:21 AM, sridhar srinivasan <
> sridhar2bioi...@gmail.com> 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: [galaxy-dev] Error in installing Galaxy.

2013-05-09 Thread Dannon Baker 
On Thu, May 9, 2013 at 12:21 AM, sridhar srinivasan <
sridhar2bioi...@gmail.com> 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: [galaxy-dev] Error in installing Galaxy.

2013-05-08 Thread 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:///

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  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
>>
>>
>>
>> __**_
>> 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/

Re: [galaxy-dev] Error in installing Galaxy.

2013-05-08 Thread 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



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___
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[galaxy-dev] Error in installing Galaxy.

2013-05-08 Thread 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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