Re: [galaxy-dev] Error in installing Galaxy.
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=galaxypassword=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 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_serverhttp://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=showredirect=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.htmlhttp://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:
Re: [galaxy-dev] Error in installing Galaxy.
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=galaxypassword=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 h...@fmi.ch
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
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=showredirect=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
Re: [galaxy-dev] Error in installing Galaxy.
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 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=galaxypassword=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 h...@fmi.ch
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
http://wiki.galaxyproject.**org/Admin/Config/Performance/**
ProductionServer?action=show**redirect=Admin%2FConfig%**
2FPerformance#Switching_to_a_**database_serverhttp://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=showredirect=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.htmlhttp://lists.bx.psu.edu/__pipermail/galaxy-dev/2010-May/__002624.html
http://lists.bx.psu.edu/**pipermail/galaxy-dev/2010-May/**002624.htmlhttp://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
Re: [galaxy-dev] Error in installing Galaxy.
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 h...@fmi.ch
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=galaxypassword=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 h...@fmi.ch
mailto:h...@fmi.ch
mailto:h...@fmi.ch 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=showredirect=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=showredirect=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
Re: [galaxy-dev] Error in installing Galaxy.
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 h...@fmi.ch 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 h...@fmi.ch 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=galaxypassword=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 h...@fmi.ch mailto:h...@fmi.ch mailto:h...@fmi.ch 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=**showredirect=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_serverhttp://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=showredirect=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.htmlhttp://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002624.html http://lists.bx.psu.edu/__**pipermail/galaxy-dev/2010-May/** __002624.htmlhttp://lists.bx.psu.edu/__pipermail/galaxy-dev/2010-May/__002624.html http://lists.bx.psu.edu/__**pipermail/galaxy-dev/2010-May/** __002624.htmlhttp://lists.bx.psu.edu/__pipermail/galaxy-dev/2010-May/__002624.html http://lists.bx.psu.edu/**pipermail/galaxy-dev/2010-May/** 002624.htmlhttp://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,
Re: [galaxy-dev] Error in installing Galaxy.
On Tue, May 21, 2013 at 7:36 AM, sridhar srinivasan sridhar2bioi...@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 ___ 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.
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 ___ 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.
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.ba...@gmail.com 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 ___ 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/
[galaxy-dev] Error in installing Galaxy.
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: [galaxy-dev] Error in installing Galaxy.
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=showredirect=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: [galaxy-dev] Error in installing Galaxy.
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_namepassword=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 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_serverhttp://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=showredirect=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.htmlhttp://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: [galaxy-dev] Error when installing galaxy - Email found in subject
Hi Dave, Thank you very much for your reply! The problem has been fixed after I installed python-boto. Regards, Jemma -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Emil Bouvier Sent: Wednesday, 28 March 2012 11:55 PM To: Jemma Wu Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Error when installing galaxy - Email found in subject Jemma, It looks like the boto package is not installed on your system. Try: sudo apt-get install python-boto Dave B. On 3/18/12 8:19 PM, Jemma Wu wrote: Dear Galaxy developers, This is the first time that I installed Galaxy on a Debian Lenny 64 bit server. I got an error of ImportError: No module named boto when I ran %sh run.sh. Please see the error message of the installation output below: File /home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 90, in app_factory add_ui_controllers( webapp, app ) File /home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 39, in add_ui_controllers module = __import__( module_name ) File /home/galaxy/galaxy-dist/lib/galaxy/web/controllers/cloud.py, line 9, in module import boto ImportError: No module named boto Does anyone know how to fix this error? Thanks in advance! Regards, Jemma ___ 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/ ___ 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/ This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. ___ 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/
Re: [galaxy-dev] Error when installing galaxy
Jemma, It looks like the boto package is not installed on your system. Try: sudo apt-get install python-boto Dave B. On 3/18/12 8:19 PM, Jemma Wu wrote: Dear Galaxy developers, This is the first time that I installed Galaxy on a Debian Lenny 64 bit server. I got an error of “ImportError: No module named boto” when I ran %sh run.sh. Please see the error message of the installation output below: File /home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 90, in app_factory add_ui_controllers( webapp, app ) File /home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 39, in add_ui_controllers module = __import__( module_name ) File /home/galaxy/galaxy-dist/lib/galaxy/web/controllers/cloud.py, line 9, in module import boto ImportError: No module named boto Does anyone know how to fix this error? Thanks in advance! Regards, Jemma ___ 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/ ___ 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/
[galaxy-dev] Error when installing galaxy
Dear Galaxy developers, This is the first time that I installed Galaxy on a Debian Lenny 64 bit server. I got an error of ImportError: No module named boto when I ran %sh run.sh. Please see the error message of the installation output below: File /home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 90, in app_factory add_ui_controllers( webapp, app ) File /home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 39, in add_ui_controllers module = __import__( module_name ) File /home/galaxy/galaxy-dist/lib/galaxy/web/controllers/cloud.py, line 9, in module import boto ImportError: No module named boto Does anyone know how to fix this error? Thanks in advance! Regards, Jemma ___ 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/
