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 <hrh@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<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

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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 <dannon.baker@gmail.com> wrote:

On Thu, May 9, 2013 at 12:21 AM, sridhar srinivasan < sridhar2bioinfo@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

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 <hrh@fmi.ch <mailto:hrh@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 <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/>

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 <hrh@fmi.ch <mailto:hrh@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 <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@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 <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/> <http://galaxyproject.org/__search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>>

On Tue, May 21, 2013 at 7:36 AM, sridhar srinivasan <sridhar2bioinfo@gmail.com> 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