Re: [galaxy-dev] problem with "~/lib/galaxy/app.py" after code upgrade to "March 12, 2012" release ('6799:40f1816d6857')

[Leandro Hermida]

Dear Hans,

>> "//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
>> line 42, in _load
>> data = list(result)[0]
>> IndexError: list index out of range

This error is because SQLAlchemy cannot load the controlled schema
version info from the DB, the result is empty, so I think its trying
to load the migrate_version and migrate_tools tables.  Make sure the
tables look like this hopefully they have each one row of data like
this:

mysql> select * from migrate_version;
+---+--+-+
| repository_id | repository_path  | version |
+---+--+-+
| Galaxy| lib/galaxy/model/migrate |  93 |
+---+--+-+
1 row in set (0.01 sec)

mysql> select * from migrate_tools;
+---+--+-+
| repository_id | repository_path  | version |
+---+--+-+
| GalaxyTools   | lib/galaxy/tool_shed/migrate |   1 |
+---+--+-+
1 row in set (0.01 sec)

hth,
Leandro

On Tue, Apr 24, 2012 at 4:09 PM, Hans-Rudolf Hotz  wrote:
> Hi everybody
>
> I usually don't like people sending the same e-mail several times, so I
> apologize for just doing this, since nobody has replied to last week's email
> so far.
>
> Although, we do not encounter any problems at the moment, I fear we will run
> into problems at a later stage (ie at the next code update). This is our
> production server.
>
> Thank you very much for any help
>
> Regards, Hans
>
>
>
>
> On 04/16/2012 03:43 PM, Hans-Rudolf Hotz wrote:
>>
>> Hi
>>
>> We are in the process of migrating our Galaxy servers to the current
>> "March 12, 2012" release ('6799:40f1816d6857').
>>
>> We have encountered two issues, which I guess are related:
>>
>>
>> If I restart the server, I get:
>>
>>
>> galaxy.model.migrate.check INFO 2012-04-16 09:24:50,391 At database
>> version 93
>> galaxy.tool_shed.migrate.check DEBUG 2012-04-16 09:24:50,407
>> MySQL_python egg successfully loaded for mysql dialect
>> Traceback (most recent call last):
>> File "//galaxy_dist/lib/galaxy/web/buildapp.py", line 82, in
>> app_factory
>> app = UniverseApplication( global_conf = global_conf, **kwargs )
>> File "//galaxy_dist/lib/galaxy/app.py", line 37, in __init__
>> verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
>> '__file__', None ), self.config.database_engine_options )
>> File "//galaxy_dist/lib/galaxy/tool_shed/migrate/check.py", line 42,
>> in verify_tools
>> db_schema = schema.ControlledSchema( engine, migrate_repository )
>> File
>>
>> "//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
>> line 24, in __init__
>> self._load()
>> File
>>
>> "//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
>> line 42, in _load
>> data = list(result)[0]
>> IndexError: list index out of range
>>
>>
>>
>> I can 'temporary' fix this by commenting-out line 36 and 37 in
>> ~/lib/galaxy/app.py
>>
>> 36# from galaxy.tool_shed.migrate.check import verify_tools
>> 37# verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
>> '__file__', None ), self.config.database_engine_options )
>>
>>
>> ...well, I don't like this fix, and I wonder if there is a better one?
>>
>>
>>
>> I have a suspicion, that this is related to problems I encountered
>> during the database schema upgrade to version 93 for our MySQL database:
>>
>> at step "90to91" and "91to92" I get the following:
>>
>>
>> 90 -> 91...
>>
>> Migration script to create the tool_version and tool_version_association
>> tables and drop the tool_id_guid_map table.
>>
>> 0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,719 Creating
>> tool_version table failed: (OperationalError) (1050, "Table
>> 'tool_version' already exists") u'\nCREATE TABLE tool_version (\n\tid
>> INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME,
>> \n\tupdate_time DATETIME, \n\ttool_id VARCHAR(255),
>> \n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN
>> KEY(tool_shed_repository_id) REFERENCES tool_shed_repository
>> (id)\n)\n\n' ()
>> 0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,719 Creating
>> tool_version table failed: (OperationalError) (1050, "Table
>> 'tool_version' already exists") u'\nCREATE TABLE tool_version (\n\tid
>> INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME,
>> \n\tupdate_time DATETIME, \n\ttool_id VARCHAR(255),
>> \n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN
>> KEY(tool_shed_repository_id) REFERENCES tool_shed_repository
>> (id)\n)\n\n' ()
>> 0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,720 Creating
>> tool_version_association table failed: (OperationalError) (1050, "Table
>> 'tool_version_association' already exists") u'\nCREATE TABLE
>> tool_version_association (\n\tid INTE

[galaxy-dev] Setting genome build on datasets transferred from sample tracking external service

[Leandro Hermida]

Dear Galaxy Dev,

Is there a way to set the genome build metadata on datasets
transferred from an external service in the sample tracking system?

-Leandro
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[galaxy-dev] "AttributeError: 'NoneType' object has no attribute 'decode'" with Dataset Actions --> Select more datasets

[Leandro Hermida]

Dear Galaxy Dev,

On the viewed transferred datasets screen, when you click on Dataset
Actions --> Select more datasets, I get the following error and stack
trace:

AttributeError: 'NoneType' object has no attribute 'decode'
URL: 
http://galaxyserver/requests_admin/select_datasets_to_transfer?cntrller=requests_admin&sample_id=f2db41e1fa331b3e&request_id=f2db41e1fa331b3e
Module weberror.evalexception.middleware:364 in respond view
>>  app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
>>  environ, self.app)
Module paste.wsgilib:539 in intercept_output view
>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
>>  return self.application(environ, start_response)
Module galaxy.web.framework.middleware.remoteuser:111 in __call__ view
>>  return self.app( environ, start_response )
Module paste.httpexceptions:632 in __call__ view
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:145 in __call__ view
>>  body = method( trans, **kwargs )
Module galaxy.web.framework:139 in decorator view
>>  return func( self, trans, *args, **kwargs )
Module galaxy.web.controllers.requests_admin:355 in
select_datasets_to_transfer view
>>  external_service = trans.sa_session.query( trans.model.ExternalService 
>> ).get( trans.security.decode_id( external_service_id ) )
Module galaxy.web.security:45 in decode_id view
>>  return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) )
AttributeError: 'NoneType' object has no attribute 'decode'
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[galaxy-dev] "UnboundLocalError: local variable 'sample' referenced before assignment" when deleting transferred datasets

[Leandro Hermida]

Dear Galaxy Dev,

There seems to be another bug in the latest galaxy-dist, when you are
on the Manage Datasets screen for a sample and you click on a few
datasets that have been transferred and associated already and try
select to delete them you get the following stack trace error:

UnboundLocalError: local variable 'sample' referenced before assignment
URL: 
http://galaxyserver/requests_admin/manage_datasets?sort=-create_time&show_item_checkboxes=false&async=false&page=1&webapp=undefined&operation=delete&id=f2db41e1fa331b3e,f597429621d6eb2b&;
Module weberror.evalexception.middleware:364 in respond view
>>  app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
>>  environ, self.app)
Module paste.wsgilib:539 in intercept_output view
>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
>>  return self.application(environ, start_response)
Module galaxy.web.framework.middleware.remoteuser:111 in __call__ view
>>  return self.app( environ, start_response )
Module paste.httpexceptions:632 in __call__ view
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:145 in __call__ view
>>  body = method( trans, **kwargs )
Module galaxy.web.framework:139 in decorator view
>>  return func( self, trans, *args, **kwargs )
Module galaxy.web.controllers.requests_admin:239 in manage_datasets view
>>  sample_id=trans.security.encode_id( sample.id ),
UnboundLocalError: local variable 'sample' referenced before assignment
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Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever

[Leandro Hermida]

Dear Galaxy Dev,

The malformed library folder error on the latest galaxy-dist I am
gettting (shown below) right after data transfer I am pretty sure is a
bug and regression.

I was just able to do the exact same sample tracking setup on one of
my other Galaxy servers which is an older galaxy-dist version from
last year and everything works ok during library folder association.

regards,
Leandro

On Wed, Mar 28, 2012 at 1:20 PM, Leandro Hermida
 wrote:
> Dear Galaxy Dev,
>
> Now I have another problem with the Galaxy sample tracking data
> transfer.  Galaxy is not able to transfer the datasets but when it
> attempts to associate the datasets with the library and folder
> specified in the sequencing request I get this:
>
> 2012-03-28 13:07:02,706 - datatx_18327 - Setting status "Adding to
> data library" for dataset "All" of sample "16"
> 2012-03-28 13:07:02,706 - datatx_18327 -
> (u'c969d2e16ec64867a127d6e3a4018b12',
> u'http://galaxydev/api/samples/1e8ab44153008be8',
> {'sample_dataset_ids': ['2f94e8ae9edff68a', '8237ee2988567c1c'],
> 'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
> 'new_status': 'Adding to data library'})
> 2012-03-28 13:07:02,817 - datatx_18327 - [200, 'Done']
> 2012-03-28 13:07:02,818 - datatx_18327 -
> (u'c969d2e16ec64867a127d6e3a4018b12',
> u'http://galaxydev/api/libraries/1e8ab44153008be8/contents',
> {'file_type': 'auto', 'server_dir':
> '/gpfshpc/data/pmrdcdb/galaxy/datatx_18327_28Mar2012', 'dbkey': '',
> 'create_type': 'file', 'folder_id':
> '994debf9f6ab02b99d7cff57c04c6b7c', 'upload_option':
> 'upload_directory'})
> 2012-03-28 13:07:02,906 - datatx_18327 - 400 Bad Request
> The server could not comply with the request since
> it is either malformed or otherwise incorrect.
>
> Malformed LibraryFolder id ( 994debf9f6ab02b99d7cff57c04c6b7c )
> specified, unable to decode
>
> What could be the problem here? Any help would be appreciated.
>
> regards,
> Leandro
>
> On Wed, Mar 28, 2012 at 1:15 PM, Leandro Hermida
>  wrote:
>> Dear Galaxy Dev,
>>
>> Ok I have gotten further found out what was going on, in my
>> data_transfer.log I was getting HTTP 404 Not Authorized when the data
>> transfer was trying to access Galaxy API URLs
>> http://galaxyserver/api/... This is because we are using external user
>> authentication as documented in
>> http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy and this puts
>> all of Galaxy behind this authentication. Since the Galaxy API uses
>> API keys to essentially authenticate you have to change you > /> ...  container to not match URLs starting with /api. To
>> do this you have to change it to  
>> .
>>
>> best,
>> leandro
>>
>> On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang  wrote:
>>> I've got the same problem and when I looked at the data_transfer.log, I saw
>>> the following message:
>>>
>>> 2012-03-01 15:12:27,338 - datatx_13870 -
>>> (u'9c17d84742cd2acb63d88b5bd41d968f',
>>> u'http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
>>> {'sample_dataset_ids': ['a799d38679e985db', '33b43b4e7093c91f'],
>>> 'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
>>> 'new_status': 'Adding to data library'})
>>> 2012-03-01 15:12:27,342 - datatx_13870 - Error. >> "-//IETF//DTD HTML 2.0//EN">
>>> 
>>> 405 Method Not Allowed
>>> 
>>> Method Not Allowed
>>> The requested method PUT is not allowed for the URL
>>> /api/samples/2d9035b3fc152403.
>>> 
>>>
>>> Using Galaxy instead of Apache as the web server changed the sample status
>>> from "in queue" to complete but didn't add the downloaded files to the data
>>> library.
>>>
>>> Luobin
>>>
>>> On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida
>>>  wrote:
>>>>
>>>> Dear Galaxy Dev,
>>>>
>>>> I've set up the Galaxy sample tracking system data transfer
>>>> functionality exactly as specified here
>>>> https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
>>>> attempt to transfer datasets it puts them into the queue and then
>>>> never seems to transfer anything.
>>>>
>>&

Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever

[Leandro Hermida]

Dear Galaxy Dev,

Now I have another problem with the Galaxy sample tracking data
transfer.  Galaxy is not able to transfer the datasets but when it
attempts to associate the datasets with the library and folder
specified in the sequencing request I get this:

2012-03-28 13:07:02,706 - datatx_18327 - Setting status "Adding to
data library" for dataset "All" of sample "16"
2012-03-28 13:07:02,706 - datatx_18327 -
(u'c969d2e16ec64867a127d6e3a4018b12',
u'http://galaxydev/api/samples/1e8ab44153008be8',
{'sample_dataset_ids': ['2f94e8ae9edff68a', '8237ee2988567c1c'],
'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
'new_status': 'Adding to data library'})
2012-03-28 13:07:02,817 - datatx_18327 - [200, 'Done']
2012-03-28 13:07:02,818 - datatx_18327 -
(u'c969d2e16ec64867a127d6e3a4018b12',
u'http://galaxydev/api/libraries/1e8ab44153008be8/contents',
{'file_type': 'auto', 'server_dir':
'/gpfshpc/data/pmrdcdb/galaxy/datatx_18327_28Mar2012', 'dbkey': '',
'create_type': 'file', 'folder_id':
'994debf9f6ab02b99d7cff57c04c6b7c', 'upload_option':
'upload_directory'})
2012-03-28 13:07:02,906 - datatx_18327 - 400 Bad Request
The server could not comply with the request since
it is either malformed or otherwise incorrect.

Malformed LibraryFolder id ( 994debf9f6ab02b99d7cff57c04c6b7c )
specified, unable to decode

What could be the problem here? Any help would be appreciated.

regards,
Leandro

On Wed, Mar 28, 2012 at 1:15 PM, Leandro Hermida
 wrote:
> Dear Galaxy Dev,
>
> Ok I have gotten further found out what was going on, in my
> data_transfer.log I was getting HTTP 404 Not Authorized when the data
> transfer was trying to access Galaxy API URLs
> http://galaxyserver/api/... This is because we are using external user
> authentication as documented in
> http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy and this puts
> all of Galaxy behind this authentication. Since the Galaxy API uses
> API keys to essentially authenticate you have to change you  /> ...  container to not match URLs starting with /api. To
> do this you have to change it to  
> .
>
> best,
> leandro
>
> On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang  wrote:
>> I've got the same problem and when I looked at the data_transfer.log, I saw
>> the following message:
>>
>> 2012-03-01 15:12:27,338 - datatx_13870 -
>> (u'9c17d84742cd2acb63d88b5bd41d968f',
>> u'http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
>> {'sample_dataset_ids': ['a799d38679e985db', '33b43b4e7093c91f'],
>> 'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
>> 'new_status': 'Adding to data library'})
>> 2012-03-01 15:12:27,342 - datatx_13870 - Error. > "-//IETF//DTD HTML 2.0//EN">
>> 
>> 405 Method Not Allowed
>> 
>> Method Not Allowed
>> The requested method PUT is not allowed for the URL
>> /api/samples/2d9035b3fc152403.
>> 
>>
>> Using Galaxy instead of Apache as the web server changed the sample status
>> from "in queue" to complete but didn't add the downloaded files to the data
>> library.
>>
>> Luobin
>>
>> On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida
>>  wrote:
>>>
>>> Dear Galaxy Dev,
>>>
>>> I've set up the Galaxy sample tracking system data transfer
>>> functionality exactly as specified here
>>> https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
>>> attempt to transfer datasets it puts them into the queue and then
>>> never seems to transfer anything.
>>>
>>> The galaxy_listener.log shows:
>>>
>>> 2012-03-26 17:16:24,515 - GalaxyAMQP - GALAXY LISTENER PID: 8738 -
>>> {'config_file': 'universe_wsgi.ini', 'http_server_section':
>>> 'server:main'}
>>> 2012-03-26 17:16:24,518 - GalaxyAMQP - {'exchange': 'galaxy_exchange',
>>> 'rabbitmqctl_path':
>>>
>>> '/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rabbitmqctl',
>>> 'userid': 'galaxy_dev', 'routing_key': 'bar_code_scanner', 'queue':
>>> 'galaxy_queue', 'host': '127.0.0.1', 'virtual_host':
>>> 'galaxy_dev_messaging_engine', 'password': 'myp

Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever

[Leandro Hermida]

Dear Galaxy Dev,

Ok I have gotten further found out what was going on, in my
data_transfer.log I was getting HTTP 404 Not Authorized when the data
transfer was trying to access Galaxy API URLs
http://galaxyserver/api/... This is because we are using external user
authentication as documented in
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy and this puts
all of Galaxy behind this authentication. Since the Galaxy API uses
API keys to essentially authenticate you have to change you  ...  container to not match URLs starting with /api. To
do this you have to change it to  
.

best,
leandro

On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang  wrote:
> I've got the same problem and when I looked at the data_transfer.log, I saw
> the following message:
>
> 2012-03-01 15:12:27,338 - datatx_13870 -
> (u'9c17d84742cd2acb63d88b5bd41d968f',
> u'http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
> {'sample_dataset_ids': ['a799d38679e985db', '33b43b4e7093c91f'],
> 'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
> 'new_status': 'Adding to data library'})
> 2012-03-01 15:12:27,342 - datatx_13870 - Error.  "-//IETF//DTD HTML 2.0//EN">
> 
> 405 Method Not Allowed
> 
> Method Not Allowed
> The requested method PUT is not allowed for the URL
> /api/samples/2d9035b3fc152403.
> 
>
> Using Galaxy instead of Apache as the web server changed the sample status
> from "in queue" to complete but didn't add the downloaded files to the data
> library.
>
> Luobin
>
> On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida
>  wrote:
>>
>> Dear Galaxy Dev,
>>
>> I've set up the Galaxy sample tracking system data transfer
>> functionality exactly as specified here
>> https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
>> attempt to transfer datasets it puts them into the queue and then
>> never seems to transfer anything.
>>
>> The galaxy_listener.log shows:
>>
>> 2012-03-26 17:16:24,515 - GalaxyAMQP - GALAXY LISTENER PID: 8738 -
>> {'config_file': 'universe_wsgi.ini', 'http_server_section':
>> 'server:main'}
>> 2012-03-26 17:16:24,518 - GalaxyAMQP - {'exchange': 'galaxy_exchange',
>> 'rabbitmqctl_path':
>>
>> '/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rabbitmqctl',
>> 'userid': 'galaxy_dev', 'routing_key': 'bar_code_scanner', 'queue':
>> 'galaxy_queue', 'host': '127.0.0.1', 'virtual_host':
>> 'galaxy_dev_messaging_engine', 'password': 'mypassword', 'port':
>> '5672'}
>> 2012-03-26 17:16:24,565 - GalaxyAMQP - Connected to rabbitmq server -
>> 127.0.0.1:5672
>> 2012-03-26 17:31:23,393 - GalaxyAMQP - MESSAGE RECVD: data_transfer
>> 2012-03-26 17:31:23,393 - GalaxyAMQP - DATA TRANSFER
>> 2012-03-26 17:31:23,401 - GalaxyAMQP - Started process (25406): python
>>
>> "/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/scripts/galaxy_messaging/server/data_transfer.py"
>> " 
>> rd-galaxydev.app.pmi
>> 69bbd1a9b18eda2a888e9963820d8ef0
>> chp723
>> galaxy
>> mypassword
>> 12
>> 12
>> 15
>> 52                    
>>  10
>> ttt_2.fastq.gz
>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz
>>          
>> 9
>> ttt_1.fastq.gz
>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz
>>                          "
>> "universe_wsgi.ini"
>>
>> The FASTQ files are for testing and aren't very big (7.6 MB), what
>> could be going wrong?
>>
>> regards,
>> Leandro
>> ___
>> 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/
>
>

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[galaxy-dev] Sample tracking data transfer hangs "in queue" forever

[Leandro Hermida]

Dear Galaxy Dev,

I've set up the Galaxy sample tracking system data transfer
functionality exactly as specified here
https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
attempt to transfer datasets it puts them into the queue and then
never seems to transfer anything.

The galaxy_listener.log shows:

2012-03-26 17:16:24,515 - GalaxyAMQP - GALAXY LISTENER PID: 8738 -
{'config_file': 'universe_wsgi.ini', 'http_server_section':
'server:main'}
2012-03-26 17:16:24,518 - GalaxyAMQP - {'exchange': 'galaxy_exchange',
'rabbitmqctl_path':
'/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rabbitmqctl',
'userid': 'galaxy_dev', 'routing_key': 'bar_code_scanner', 'queue':
'galaxy_queue', 'host': '127.0.0.1', 'virtual_host':
'galaxy_dev_messaging_engine', 'password': 'mypassword', 'port':
'5672'}
2012-03-26 17:16:24,565 - GalaxyAMQP - Connected to rabbitmq server -
127.0.0.1:5672
2012-03-26 17:31:23,393 - GalaxyAMQP - MESSAGE RECVD: data_transfer
2012-03-26 17:31:23,393 - GalaxyAMQP - DATA TRANSFER
2012-03-26 17:31:23,401 - GalaxyAMQP - Started process (25406): python
"/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/scripts/galaxy_messaging/server/data_transfer.py"
" 
rd-galaxydev.app.pmi
69bbd1a9b18eda2a888e9963820d8ef0
chp723
galaxy
mypassword
12
12
15
52
  10
ttt_2.fastq.gz
/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz
  
9
ttt_1.fastq.gz
/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz
  "
"universe_wsgi.ini"

The FASTQ files are for testing and aren't very big (7.6 MB), what
could be going wrong?

regards,
Leandro
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[galaxy-dev] Normal that latest galaxy-dist creates shed_tools directory one level up from the galaxy-dist directory?

[Leandro Hermida]

Dear all,

Is it normal that the latest galaxy-dist creates a shed_tools
directory one directory up (and outside) from the server galaxy-dist
directory?

best,
Leandro
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[galaxy-dev] New Galaxy look from usegalaxy.org

[Leandro Hermida]

Dear all,

How do I get the new Galaxy look enabled that you see in
usegalaxy.org? I have two servers on the latest galaxy-dist.

regards,
Leandro
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[galaxy-dev] Galaxy AMQP listener startup script error

[Leandro Hermida]

Dear all,

I followed the directions in
https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer to set up the
Galaxy AMQP listener service so that the sample tracking system can
transfer datasets. When running

nohup sh run_galaxy_listener.sh &

Traceback (most recent call last):
  File "scripts/galaxy_messaging/server/amqp_consumer.py", line 33, in 
from galaxy.web.api.requests import RequestsAPIController
  File 
"/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/lib/galaxy/web/api/requests.py",
line 7, in 
from galaxy.web.base.controller import *
  File 
"/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/lib/galaxy/web/base/controller.py",
line 17, in 
from galaxy.visualization.tracks.data_providers import get_data_provider
  File 
"/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/lib/galaxy/visualization/tracks/data_providers.py",
line 11, in 
pkg_resources.require( "pysam" )
  File 
"/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/lib/galaxy/eggs/__init__.py",
line 415, in require
raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) )
galaxy.eggs.EggNotFetchable: ['pysam']

But Galaxy runs fine and the pysam eggs are already there for a long
time as they are used by Galaxy. What could be the problem?

kind regards,
Leandro
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Re: [galaxy-dev] refresh_on_change is broken?

[Leandro Hermida]

Dear Greg,

On Wed, Mar 21, 2012 at 3:20 PM, Greg Von Kuster  wrote:
> Leandro,
>
> For refresh_on_change to work you need a set of optional selections and a
> set of refresh_on_change values, so in your example, the type should
> probably be a select instead of data.  You'll also need the select list
> options to be generated based on your history items (at least that's what I
> think you're attempt here), so your list of refresh_on_change values will be
> attributes of those history items.
>
> Greg Von Kuster

Could you show an example of this functionality that you described?
This is new to me I really apologize and I looked for things on the
Galaxy wiki but couldn't find. How would one do the simple example I
illustrated in this thread:






Where in the tool form if the user changes the first drop-down menu to
select a different file of a particular format from their history it
will cause a refresh of the page so that the dynamic_options function
in the second menu can be re-executed using the new file name as a
parameter then generating new options in this second menu?

regards,
Leandro

>
> On Mar 21, 2012, at 9:27 AM, Leandro Hermida wrote:
>
>
> Here's one example:
>
>
> 
>
>    
> label="Select a file from you history" />
>
>    
> dynamic_options="get_options_from_file(dataset.file_name)" />
>
> 
>
>
> If the user changes their selection of data from their history it
>
> should refresh the page and call the dynamic options again to load the
>
> other select menu with the choices from the new file. Currently you
>
> have to do this with repeat or pages tags which is really cumbersome
>
> for the user in the UI or doesn't allow workflowing, respectively.
>
>
>
> Page should refresh automatically when dataset is changed and dynamic
>
> options are used. If not, it's a bug.
>
>
> Ok, not sure what this means, the above example I wrote doesn't work
> so is this a bug or is there another way to write the above example so
> that it will work?
>
> regards,
> Leandro
>
>
>
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>

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Re: [galaxy-dev] refresh_on_change is broken?

[Leandro Hermida]

Dear Jeremy,

On Wed, Mar 21, 2012 at 1:37 PM, Jeremy Goecks  wrote:
>
> Maybe we don't understand the feature in the documentation, but this
> isn't the refresh_on_change functionality. In the Tophat tool XML
> there are no refresh_on_change="true" attributes, you are talking
> about a conditional tag which when changing will refresh the page in
> order to expose different parts of a form depending on then value
> chosen, this is a different use case.
>
>
> The conditional tag has "refresh_on_change" added automatically and is used
> by Javascript accordingly.
>

This is understood, we use conditionals all the time, just was trying
to explain that conditionals are only for certain use cases when you
need to expose/hide different form elements depending on changing of a
parameter. Yet there are other use cases when you need
refresh_on_change functionality and not a conditional.

> The feature we thought exists from the wiki docs is a utility
> refresh_on_change="true" attribute that you can put on any input param
> tag which will cause the page to refresh with the changed state when
> you change the param. It's supposed to replace the deprecated pages
> tags.
>
> Unless there is undocumented functionality, refresh_on_change cannot be
> explicitly used:
>
> http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
>
>
> Once we started needing to make more complex form logic you
> realize that this is not just very useful but necessary.
>
> Here's one example:
>
> 
>     label="Select a file from you history" />
>     dynamic_options="get_options_from_file(dataset.file_name)" />
> 
>
> If the user changes their selection of data from their history it
> should refresh the page and call the dynamic options again to load the
> other select menu with the choices from the new file. Currently you
> have to do this with repeat or pages tags which is really cumbersome
> for the user in the UI or doesn't allow workflowing, respectively.
>
>
> Page should refresh automatically when dataset is changed and dynamic
> options are used. If not, it's a bug.

Ok, not sure what this means, the above example I wrote doesn't work
so is this a bug or is there another way to write the above example so
that it will work?

regards,
Leandro

>
> J.
>
>
> Does this feature I describe to replace the deprecated pages tags not
> exist or just isn't fully implemented yet?
>
> regards,
> Leandro
>
> Some questions that should shed light on your issues:
>
> *Does the Tophat tool refresh on the main server? If not, this is probably a
> browser issue.
>
> *Are you seeing any errors in the Javascript console?
>
> *Can you be more specific about what problems you're seeing and whether you
> can reproduce with known tools?
>
>
> Thanks,
>
> J.
>
>
> On Mar 20, 2012, at 9:28 AM, Leandro Hermida wrote:
>
>
> Hi everyone,
>
>
> Sorry to ping again, having the refresh_on_change functionality not
>
> working in Galaxy has us making tool forms in ways we really don't
>
> want to,
>
>
> no one needs to use refresh_on_change or am I the only one that finds
>
> it's broken? We've started to look at what Galaxy is trying to do,
>
> seems like you are using jQuery to bind a custom Javascript
>
> refresh_on_change function but when you look at that function it
>
> doesn't do any form reloading, maybe just the feature is unfinished?
>
>
> sincerely,
>
> Leandro
>
>
>
> On Wed, Feb 29, 2012 at 10:34 AM, Leandro Hermida
>
>  wrote:
>
> Hello,
>
>
> Seems like the refresh_on_change functionality is broken in the latest
>
> galaxy-dist.  If you apply it to an input parameter it doesn't seem to
>
> refresh the page when you change the selection of that parameter. Does
>
> anyone else also have the problem?
>
>
> regards,
>
> Leandro
>
>

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Re: [galaxy-dev] refresh_on_change is broken?

[Leandro Hermida]

Dear Jeremy,

On Tue, Mar 20, 2012 at 6:19 PM, Jeremy Goecks  wrote:
> Leandro,
>
> refresh_on_change is used quite a bit throughout the tool UI and appears to 
> work fine both on a local instance and on the public instance. E.g. look at 
> Tophat and change settings from 'Use Defaults' to 'Full Parameter List' -- 
> the refresh_on_change works on reload the tool with more parameters.
>

Maybe we don't understand the feature in the documentation, but this
isn't the refresh_on_change functionality. In the Tophat tool XML
there are no refresh_on_change="true" attributes, you are talking
about a conditional tag which when changing will refresh the page in
order to expose different parts of a form depending on then value
chosen, this is a different use case.

The feature we thought exists from the wiki docs is a utility
refresh_on_change="true" attribute that you can put on any input param
tag which will cause the page to refresh with the changed state when
you change the param. It's supposed to replace the deprecated pages
tags.  Once we started needing to make more complex form logic you
realize that this is not just very useful but necessary.

Here's one example:


   
   


If the user changes their selection of data from their history it
should refresh the page and call the dynamic options again to load the
other select menu with the choices from the new file. Currently you
have to do this with repeat or pages tags which is really cumbersome
for the user in the UI or doesn't allow workflowing, respectively.

Does this feature I describe to replace the deprecated pages tags not
exist or just isn't fully implemented yet?

regards,
Leandro

> Some questions that should shed light on your issues:
> *Does the Tophat tool refresh on the main server? If not, this is probably a 
> browser issue.
> *Are you seeing any errors in the Javascript console?
> *Can you be more specific about what problems you're seeing and whether you 
> can reproduce with known tools?
>
> Thanks,
> J.
>
> On Mar 20, 2012, at 9:28 AM, Leandro Hermida wrote:
>
>> Hi everyone,
>>
>> Sorry to ping again, having the refresh_on_change functionality not
>> working in Galaxy has us making tool forms in ways we really don't
>> want to,
>>
>> no one needs to use refresh_on_change or am I the only one that finds
>> it's broken? We've started to look at what Galaxy is trying to do,
>> seems like you are using jQuery to bind a custom Javascript
>> refresh_on_change function but when you look at that function it
>> doesn't do any form reloading, maybe just the feature is unfinished?
>>
>> sincerely,
>> Leandro
>>
>>
>> On Wed, Feb 29, 2012 at 10:34 AM, Leandro Hermida
>>  wrote:
>>> Hello,
>>>
>>> Seems like the refresh_on_change functionality is broken in the latest
>>> galaxy-dist.  If you apply it to an input parameter it doesn't seem to
>>> refresh the page when you change the selection of that parameter. Does
>>> anyone else also have the problem?
>>>
>>> regards,
>>> Leandro
>>
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>>  http://lists.bx.psu.edu/
>

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Re: [galaxy-dev] refresh_on_change is broken?

[Leandro Hermida]

Hi everyone,

Sorry to ping again, having the refresh_on_change functionality not
working in Galaxy has us making tool forms in ways we really don't
want to,

no one needs to use refresh_on_change or am I the only one that finds
it's broken? We've started to look at what Galaxy is trying to do,
seems like you are using jQuery to bind a custom Javascript
refresh_on_change function but when you look at that function it
doesn't do any form reloading, maybe just the feature is unfinished?

sincerely,
Leandro


On Wed, Feb 29, 2012 at 10:34 AM, Leandro Hermida
 wrote:
> Hello,
>
> Seems like the refresh_on_change functionality is broken in the latest
> galaxy-dist.  If you apply it to an input parameter it doesn't seem to
> refresh the page when you change the selection of that parameter. Does
> anyone else also have the problem?
>
> regards,
> Leandro

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Re: [galaxy-dev] bug with Galaxy form validation and dynamic_options population of drop-down menus where option values are integers

[Leandro Hermida]

Hi all,

Thanks Hans for giving a hint as to what we might need to try, we
tried pasing True and False for the is selected field and the Galaxy
form validation still doesn't like it, turns out it's the option value
fields that have to be stringified in your JSON encoder so that you
JSON reads:

["One", "1", True ],
["Two", "2", False ],

Hope this helps others with the same issue, if you want to pass
numbers as the option values make sure to stringify them.

regards,
Leandro

On Thu, Mar 1, 2012 at 10:34 AM, Hans-Rudolf Hotz  wrote:
> Hi Leandro
>
> Although we use 'dynamic_options' successfully in many tools, it is still a
> little mystery to me sometimes - probably due to my non-existing python
> knowledge.
>
> Hence just double checking:
>
> Does  [ "One",1,True ],
>      [ "Two",2,False ],
>      [ "Three",3,False]
>                          work?
>
>
> Regards, Hans
>
>
> On 02/29/2012 04:44 PM, Leandro Hermida wrote:
>>
>> Hello,
>>
>> If you have a form with an input like this:
>>
>> 
>>
>> And the options dynamically generated have integers as values, e.g.
>> options tuples like this:
>>
>> [ "One", 1, 1 ],
>> [ "Two", 2, 0 ],
>> [ "Three", 3, 0 ]
>>
>> When you try to submit the galaxy form you always get the validation
>> error  "An invalid option was selected, please verify".
>>
>> regards,
>> Leandro
>> ___
>> 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/

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Re: [galaxy-dev] uploads stuck in history

[Leandro Hermida]

Hello,

We don't use the nginx module

kind regards,
Leandro

On Wed, Mar 7, 2012 at 4:42 PM, Jorrit Boekel
 wrote:
> Hi Nate,
>
> I wasn't before, but I switched to nginx now. Non-uploading is still
> happening in firefox (10.0.2 on ubuntu 11.10).
>
> I can't be 100% sure that my nginx install was correct, but it's definitely
> serving galaxy and not complaining. Is there any way to verify uploads are
> processed through nginx?
>
> jorrit
>
>
>
> On 03/05/2012 08:37 PM, Nate Coraor wrote:
>>
>> By any chance, do you all happen to be using the nginx upload module?  I
>> am guessing not.
>>
>> --nate
>>
>> On Feb 23, 2012, at 3:16 AM, Bossers, Alex wrote:
>>
>>> I confirm the same strange behaviour since some of the last updates on
>>> the central version. We are at the latest now.
>>> It is also with medium (10Mb+ tarballs) AND large files! Furthermore its
>>> seems to be in FireFox only They upload fine using IE8 or 9. Didn't test
>>> other browsers though.
>>>
>>> Annoying it is indeed.
>>>
>>> Alex
>>>
>>>
>>> -Oorspronkelijk bericht-
>>> Van: galaxy-dev-boun...@lists.bx.psu.edu
>>> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Jorrit Boekel
>>> Verzonden: woensdag 22 februari 2012 10:15
>>> Aan: galaxy-dev@lists.bx.psu.edu
>>> Onderwerp: [galaxy-dev] uploads stuck in history
>>>
>>> Dear list,
>>>
>>> I have stumbled on some strange behaviour when uploading files to galaxy
>>> via the upload.py tool. At times, the upload seems to be stalled in history
>>> and is never actually performed, followed by a seemingly infinite history
>>> update (see log below). My system is Ubuntu 11.10 and runs Python 2.7.2. I
>>> find the behaviour in both my own modified galaxy install (based on
>>> galaxy-dist), and in a fresh clone from galaxy-central.
>>>
>>> I have tried to upload different files, and all seem to sometimes trigger
>>> the behaviour, but not all the time. A restart of galaxy sometimes sorts
>>> things out. Common for the debug messages is that it seems there is never a
>>> job id generated as in "galaxy.tools.actions.upload_common INFO 2012-02-22
>>> 10:06:36,186 tool
>>> upload1 created job id 2".
>>>
>>> Has anyone seen similar things or can it be a problem with my system?
>>>
>>> cheers,
>>> jorrit
>>>
>>>
>>>
>>>
>>>
>>>
>>> --Debug messa:
>>>
>>> galaxy.web.framework DEBUG 2012-02-22 09:47:43,730 Error: this request
>>> returned None from get_history(): http://localhost:8080/
>>> 127.0.0.1 - - [22/Feb/2012:09:47:43 +0200] "GET / HTTP/1.1" 200 - "-"
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101
>>> Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /root/tool_menu HTTP/1.1"
>>> 200 - "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /history HTTP/1.1" 200 -
>>> "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "POST /root/user_get_usage
>>> HTTP/1.1" 200 - "http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu;
>>> Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:47:50 +0200] "GET
>>> /tool_runner?tool_id=upload1 HTTP/1.1" 200 -
>>> "http://localhost:8080/root/tool_menu"; "Mozilla/5.0 (X11; Ubuntu; Linux
>>> x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST
>>> /tool_runner/upload_async_create HTTP/1.1" 200 - "http://localhost:8080/";
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET
>>> /tool_runner/upload_async_message HTTP/1.1" 200 - "http://localhost:8080/";
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET /history HTTP/1.1" 200 -
>>> "http://localhost:8080/tool_runner/upload_async_message"; "Mozilla/5.0 (X11;
>>> Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST /root/user_get_usage
>>> HTTP/1.1" 200 - "http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu;
>>> Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:13 +0200] "GET
>>> /tool_runner?tool_id=upload1 HTTP/1.1" 200 -
>>> "http://localhost:8080/root/tool_menu"; "Mozilla/5.0 (X11; Ubuntu; Linux
>>> x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:15 +0200] "POST
>>> /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history";
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:19 +0200] "POST
>>> /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history";
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>>> rv:10.0.2) 

Re: [galaxy-dev] bug with Galaxy form validation and dynamic_options population of drop-down menus where option values are integers

[Leandro Hermida]

Hi Hans!

Hey hope you liked the manuscript and hope to get feedback soon, yes
it seems with Galaxy when you use the dynamic_options feature to load
options into the form it seems to go through different code when
processing then statically set options in the tool XML, even though it
really shouldn't its just generating form HTML in the end and when you
hit submit to process what the user has selected they should be
completely decoupled :-/

I'll try your suggestions below today is a public holiday in Neuchatel
so will be at work tomorrow.

take care,
leandro

On Thu, Mar 1, 2012 at 10:34 AM, Hans-Rudolf Hotz  wrote:
> Hi Leandro
>
> Although we use 'dynamic_options' successfully in many tools, it is still a
> little mystery to me sometimes - probably due to my non-existing python
> knowledge.
>
> Hence just double checking:
>
> Does  [ "One",1,True ],
>      [ "Two",2,False ],
>      [ "Three",3,False]
>                          work?
>
>
> Regards, Hans
>
>
> On 02/29/2012 04:44 PM, Leandro Hermida wrote:
>>
>> Hello,
>>
>> If you have a form with an input like this:
>>
>> 
>>
>> And the options dynamically generated have integers as values, e.g.
>> options tuples like this:
>>
>> [ "One", 1, 1 ],
>> [ "Two", 2, 0 ],
>> [ "Three", 3, 0 ]
>>
>> When you try to submit the galaxy form you always get the validation
>> error  "An invalid option was selected, please verify".
>>
>> regards,
>> Leandro
>> ___
>> 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/

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[galaxy-dev] bug with Galaxy form validation and dynamic_options population of drop-down menus where option values are integers

[Leandro Hermida]

Hello,

If you have a form with an input like this:



And the options dynamically generated have integers as values, e.g.
options tuples like this:

[ "One", 1, 1 ],
[ "Two", 2, 0 ],
[ "Three", 3, 0 ]

When you try to submit the galaxy form you always get the validation
error  "An invalid option was selected, please verify".

regards,
Leandro
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[galaxy-dev] refresh_on_change is broken?

[Leandro Hermida]

Hello,

Seems like the refresh_on_change functionality is broken in the latest
galaxy-dist.  If you apply it to an input parameter it doesn't seem to
refresh the page when you change the selection of that parameter. Does
anyone else also have the problem?

regards,
Leandro
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[galaxy-dev] can the sample tracking system transfer (copy) data to a dataset library not in private Galaxy server data directory tree and then just link files?

[Leandro Hermida]

Dear all,

Is there a way with the Galaxy sample tracking system to have the
dataset transfer feature copy data to a dataset library outside the
private Galaxy server data directory tree and then the dataset library
just link (like you can do with upload files feature when managing
data libraries)?  The reason for this is that it is common to have
such huge data also available outside of Galaxy on the filesystem for
bioinformatians/computational biologists to access directly without
having to have two copies.

regards,
Leandro
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Re: [galaxy-dev] uploads stuck in history

[Leandro Hermida]

Hi all,

We get the behavior mentioned some times too, its not reproducible
just like you mentioned.  Some times it happens with small files, some
times with large files and again as you said it doesn't happen all the
time.

Now I haven't seen this yet on our Galaxy dev server which is the
latest galaxy-dist, only see this on our Galaxy production which is an
older version of galaxy-dist from last winter.

regards,
Leandro

On Wed, Feb 22, 2012 at 3:59 PM, Hans-Rudolf Hotz  wrote:
> Hi
>
> I guess we see similar things: a new history item is created, it turns
> purple, stays like this apparently forever while no job id is created (ie I
> don't see the job in any of the report tools).
>
> To be honest we ignore them, because:
>
> a) it only (as far as I can tell) happens with big data files (we try to
> avoid this anyway by using 'Data libraries') while there is heavy load on
> the storage system
>
> b) ...eventually, unless the user has deleted the history item, it does turn
> green and the job is listed as 'ok'.
>
>
> Do you experience this problem with all files, even small ones?
>
>
> Regards, Hans
>
>
>
> On 02/22/2012 10:14 AM, Jorrit Boekel wrote:
>>
>> Dear list,
>>
>> I have stumbled on some strange behaviour when uploading files to galaxy
>> via the upload.py tool. At times, the upload seems to be stalled in
>> history and is never actually performed, followed by a seemingly
>> infinite history update (see log below). My system is Ubuntu 11.10 and
>> runs Python 2.7.2. I find the behaviour in both my own modified galaxy
>> install (based on galaxy-dist), and in a fresh clone from galaxy-central.
>>
>> I have tried to upload different files, and all seem to sometimes
>> trigger the behaviour, but not all the time. A restart of galaxy
>> sometimes sorts things out. Common for the debug messages is that it
>> seems there is never a job id generated as in
>> "galaxy.tools.actions.upload_common INFO 2012-02-22 10:06:36,186 tool
>> upload1 created job id 2".
>>
>> Has anyone seen similar things or can it be a problem with my system?
>>
>> cheers,
>> jorrit
>>
>>
>>
>>
>>
>>
>> --Debug messa:
>>
>> galaxy.web.framework DEBUG 2012-02-22 09:47:43,730 Error: this request
>> returned None from get_history(): http://localhost:8080/
>> 127.0.0.1 - - [22/Feb/2012:09:47:43 +0200] "GET / HTTP/1.1" 200 - "-"
>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101
>> Firefox/10.0.2"
>> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /root/tool_menu
>> HTTP/1.1" 200 - "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu;
>> Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /history HTTP/1.1" 200 -
>> "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "POST /root/user_get_usage
>> HTTP/1.1" 200 - "http://localhost:8080/history"; "Mozilla/5.0 (X11;
>> Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>> 127.0.0.1 - - [22/Feb/2012:09:47:50 +0200] "GET
>> /tool_runner?tool_id=upload1 HTTP/1.1" 200 -
>> "http://localhost:8080/root/tool_menu"; "Mozilla/5.0 (X11; Ubuntu; Linux
>> x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST
>> /tool_runner/upload_async_create HTTP/1.1" 200 -
>> "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET
>> /tool_runner/upload_async_message HTTP/1.1" 200 -
>> "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET /history HTTP/1.1" 200 -
>> "http://localhost:8080/tool_runner/upload_async_message"; "Mozilla/5.0
>> (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST /root/user_get_usage
>> HTTP/1.1" 200 - "http://localhost:8080/history"; "Mozilla/5.0 (X11;
>> Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>> 127.0.0.1 - - [22/Feb/2012:09:48:13 +0200] "GET
>> /tool_runner?tool_id=upload1 HTTP/1.1" 200 -
>> "http://localhost:8080/root/tool_menu"; "Mozilla/5.0 (X11; Ubuntu; Linux
>> x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>> 127.0.0.1 - - [22/Feb/2012:09:48:15 +0200] "POST
>> /root/history_item_updates HTTP/1.1" 200 -
>> "http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>> 127.0.0.1 - - [22/Feb/2012:09:48:19 +0200] "POST
>> /root/history_item_updates HTTP/1.1" 200 -
>> "http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>> 127.0.0.1 - - [22/Feb/2012:09:48:23 +0200] "POST
>> /root/history_item_updates HTTP/1.1" 200 -
>> "http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>> rv:10.0.2)

[galaxy-dev] Illumina HiSeq 2000 external service type XML

[Leandro Hermida]

Hi everyone,

Does anyone have a typical external service type XML file for an
Illumina HiSeq 2000?  I have created one but not sure if its correct
and there is no guide for creating the external service type XMLs

thanks,
Leandros
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[galaxy-dev] Tool syntax to embed external web page doesn't quite work as desired anymore

[Leandro Hermida]

Hi everyone,

It used to be in the previous or so galaxy-dist that if you wanted to
have a tool which displayed a web page from another web app in the
center Galaxy frame you simply did:


from External App
http://my/url/path"; check_values="false" method="get" />


But this doesn't work anymore, instead you get a form with an
"Execute" button which you then have to click on in order to go to the
external web page you wanted to embed. How do I get the old desired
behavior?

regards,
Leandro
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[galaxy-dev] input param with type="data" multiple="true" working?

[Leandro Hermida]

Hello,

There have been previous requests/questions (some mine) about fixing Galaxy
tool functionality to enable a multiple select menu item for input data in
the history with the following:



Instead of using the cumbersome  tags and resulting form.  Is this
working in the latest Galaxy build?

kind regards,
Leandro
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Re: [galaxy-dev] problem with "Input dataset" workflow control feature and custom non-subclass datatypes

[Leandro Hermida]

Hi Dannon,

Thanks I'm glad you could reproduce it! One thing I was thinking about
since you are working in that code area is whether you could make it that
the Input Dataset workflow control feature is not required. When you use
this feature it cannot filter out the dataset history for a particular
datatype, although when don't use it and start a workflow with a tool that
has an input data parameter it is able to filter out for the desired
datatype.  It used to be in old galaxy-dist versions that if you didn't
start with the Input Dataset control feature then you couldn't use the
multiple input files workflow parallelization feature but now it doesn't
seem to be the case which is very good.

thanks,
Leandro

On Wed, Jan 25, 2012 at 2:55 PM, Dannon Baker  wrote:

> Leandro,
>
> Thanks for reporting this, I'm able to reproduce it and will let you know
> when I have a fix.
>
> -Dannon
>
>
> On Jan 20, 2012, at 11:07 AM, Leandro Hermida wrote:
>
> > Hi,
> >
> > There seems to be a weird bug with the "Input dataset" workflow
> > control feature, hard to explain clearly but I'll try my best.
> >
> > If you define a custom datatype that is a simple subclass of an
> > existing galaxy datatype, e.g.:
> >
> >  > subclass="True" display_in_upload="true"/>
> >
> > And if this datatype will be the input to a workflow where you want to
> > use the multiple input files feature you must put into your workflow
> > editor an "Input dataset" box at the beginning and connect it.
> >
> > If you define a custom datatype that's it's own custom class, e.g.:
> >
> >  > display_in_upload="true"/>
> >
> > with a simple class in lib/galaxy/datatypes/data.py e.g.:
> >
> > class MyExt( Data ):
> >file_ext = "myext"
> >
> > And if this datatype will be the input data to a workflow if you have
> > an "Input dataset" box at the beginning for some reason the drop-down
> > menu (or multi-select) won't not have files of this type from your
> > history it just ignores them. Now what is strange is if I edit the
> > workflow and remove the beginning "Input dataset" box and start the
> > workflow with just the first tool which has this custom datatype as an
> > input parameter then when I try to run the workflow everything shows
> > up properly :-/
> >
> > Hope I explained this ok, seems like something is broken with the
> > "Input dataset" workflow control feature.
> >
> > best,
> > Leandro
> > ___
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>
>
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[galaxy-dev] Problem running purge_datasets.sh cleanup scripts

[Leandro Hermida]

Hello,

In the latest galaxy-dist version when running the system cleanup commands
in the documented order I get an error when running the purge_datasets.sh
script:

sh delete_userless_histories.sh
sh purge_histories.sh
sh purge_libraries.sh
sh purge_folders.sh
sh delete_datasets.sh
sh purge_datasets.sh
Traceback (most recent call last):
 File "./scripts/cleanup_datasets/cleanup_datasets.py", line 518, in

   if __name__ == "__main__": main()
 File "./scripts/cleanup_datasets/cleanup_datasets.py", line 116, in main
   purge_datasets( app, cutoff_time, options.remove_from_disk, info_only =
options.info_only, force_retry = options.force_retry )
 File "./scripts/cleanup_datasets/cleanup_datasets.py", line 353, in
purge_datasets
   _purge_dataset( app, dataset, remove_from_disk, info_only = info_only )
 File "./scripts/cleanup_datasets/cleanup_datasets.py", line 478, in
_purge_dataset
   print "Error attempting to purge data file: ", dataset.file_name, "
error: ", str( exc )
 File
"/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/lib/galaxy/model/__init__.py",
line 651, in get_file_name
   assert self.object_store is not None, "Object Store has not been
initialized for dataset %s" % self.id
AssertionError: Object Store has not been initialized for dataset 58

What could be going wrong?

regards,
Leandro
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[galaxy-dev] problem with "Input dataset" workflow control feature and custom non-subclass datatypes

[Leandro Hermida]

Hi,

There seems to be a weird bug with the "Input dataset" workflow
control feature, hard to explain clearly but I'll try my best.

If you define a custom datatype that is a simple subclass of an
existing galaxy datatype, e.g.:



And if this datatype will be the input to a workflow where you want to
use the multiple input files feature you must put into your workflow
editor an "Input dataset" box at the beginning and connect it.

If you define a custom datatype that's it's own custom class, e.g.:



with a simple class in lib/galaxy/datatypes/data.py e.g.:

class MyExt( Data ):
file_ext = "myext"

And if this datatype will be the input data to a workflow if you have
an "Input dataset" box at the beginning for some reason the drop-down
menu (or multi-select) won't not have files of this type from your
history it just ignores them. Now what is strange is if I edit the
workflow and remove the beginning "Input dataset" box and start the
workflow with just the first tool which has this custom datatype as an
input parameter then when I try to run the workflow everything shows
up properly :-/

Hope I explained this ok, seems like something is broken with the
"Input dataset" workflow control feature.

best,
Leandro
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Re: [galaxy-dev] .gz extension gets stripped off when uploading via data library Upload via filesystem paths but not via Get Data -> Upload File

[Leandro Hermida]

Hi Greg,

Ok this code change to library_common.py works, now when you use the
data libraries menu to bring in .fastq.gz files it doesn't cut off the
.gz thank you!

best,
Leandro

On Fri, Jan 20, 2012 at 3:32 PM, Greg Von Kuster  wrote:
> Hello Leandro,
>
> I believe this behavior is due to the make_library_uploaded_dataset() method
> in the ~/lib/galaxy/web/controllers/library_common controller.  The current
> method looks like this:
>
>     def make_library_uploaded_dataset( self, trans, cntrller, params, name,
> path, type, library_bunch, in_folder=None ):
>         library_bunch.replace_dataset = None # not valid for these types of
> upload
>         uploaded_dataset = util.bunch.Bunch()
>         # Remove compressed file extensions, if any
>         new_name = name
>         if new_name.endswith( '.gz' ):
>             new_name = new_name.rstrip( '.gz' )
>         elif new_name.endswith( '.zip' ):
>             new_name = new_name.rstrip( '.zip' )
>         uploaded_dataset.name = new_name
>         uploaded_dataset.path = path
>         uploaded_dataset.type = type
>         uploaded_dataset.ext = None
>         uploaded_dataset.file_type = params.file_type
>         uploaded_dataset.dbkey = params.dbkey
>         uploaded_dataset.space_to_tab = params.space_to_tab
>         if in_folder:
>             uploaded_dataset.in_folder = in_folder
>         uploaded_dataset.data = upload_common.new_upload( trans, cntrller,
> uploaded_dataset, library_bunch )
>         link_data_only = params.get( 'link_data_only', 'copy_files' )
>         uploaded_dataset.link_data_only = link_data_only
>         if link_data_only == 'link_to_files':
>             uploaded_dataset.data.file_name = os.path.abspath( path )
>             # Since we are not copying the file into Galaxy's managed
>             # default file location, the dataset should never be purgable.
>             uploaded_dataset.data.dataset.purgable = False
>             trans.sa_session.add_all( ( uploaded_dataset.data,
> uploaded_dataset.data.dataset ) )
>             trans.sa_session.flush()
>         return uploaded_dataset
>
> Here are the code changes that I believe will resolve the issue.  However, I
> have not tested this, so if you wouldn't mind letting me know if this works
> for you, I'll commit the changes to the central repo.
>
>     def make_library_uploaded_dataset( self, trans, cntrller, params, name,
> path, type, library_bunch, in_folder=None ):
>         link_data_only = params.get( 'link_data_only', 'copy_files' )
>         library_bunch.replace_dataset = None # not valid for these types of
> upload
>         uploaded_dataset = util.bunch.Bunch()
>         new_name = name
>         # Remove compressed file extensions, if any, but only if
>         # we're copying files into Galaxy's file space.
>         if link_data_only == 'copy_files':
>             if new_name.endswith( '.gz' ):
>                 new_name = new_name.rstrip( '.gz' )
>             elif new_name.endswith( '.zip' ):
>                 new_name = new_name.rstrip( '.zip' )
>         uploaded_dataset.name = new_name
>         uploaded_dataset.path = path
>         uploaded_dataset.type = type
>         uploaded_dataset.ext = None
>         uploaded_dataset.file_type = params.file_type
>         uploaded_dataset.dbkey = params.dbkey
>         uploaded_dataset.space_to_tab = params.space_to_tab
>         if in_folder:
>             uploaded_dataset.in_folder = in_folder
>         uploaded_dataset.data = upload_common.new_upload( trans, cntrller,
> uploaded_dataset, library_bunch )
>         uploaded_dataset.link_data_only = link_data_only
>         if link_data_only == 'link_to_files':
>             uploaded_dataset.data.file_name = os.path.abspath( path )
>             # Since we are not copying the file into Galaxy's managed
>             # default file location, the dataset should never be purgable.
>             uploaded_dataset.data.dataset.purgable = False
>             trans.sa_session.add_all( ( uploaded_dataset.data,
> uploaded_dataset.data.dataset ) )
>             trans.sa_session.flush()
>         return uploaded_dataset
>
>
> Thanks!
>
> Greg
>
>
> On Jan 20, 2012, at 7:42 AM, Leandro Hermida wrote:
>
> Hello,
>
> We've created a new binary datatype for .fastq.gz files following the
> same methodology as the BAM files since we don't want our fasta.gz
> files to be gunzipped.  I added the appropriate code in upload.py to
> make sure of this.  This

Re: [galaxy-dev] .gz extension gets stripped off when uploading via data library Upload via filesystem paths but not via Get Data -> Upload File

[Leandro Hermida]

Hi Peter,

Sorry I wasn't clear, the .gz gets stripped from the name in the
Galaxy UI when you upload the files into a data library via the manage
data libraries form. When you upload it via Get Data -> Upload File
the .gz is preserved which is what one would want since I am not
having it gunzipped by specifying its own new datatype and extension
and changing binary.py to make sure it doesn't fall through to the
elsif where it tries to unzip stuff.

On Fri, Jan 20, 2012 at 2:25 PM, Peter Cock  wrote:
> On Fri, Jan 20, 2012 at 12:42 PM, Leandro Hermida
>  wrote:
>> Hello,
>>
>> We've created a new binary datatype for .fastq.gz files following the
>> same methodology as the BAM files since we don't want our fasta.gz
>> files to be gunzipped.  I added the appropriate code in upload.py to
>> make sure of this.  This new datatype and extension successfully does
>> not gunzip our files.  But when we upload it into a data library via
>> the data library "Upload via filesystem paths" it for some reason
>> automatically strips the .gz part out. When we take the same .fastq.gz
>> file and upload it via Get Data -> Upload File it works fine, nothing
>> is stripped from file name. Where is it doing this and how can prevent
>> from stripping the .gz via the data library menus?
>
> I thought Galaxy would usually try to replace the extension
> with *.dat for any file type when uploaded?
>
> Peter
>
> P.S. Is anyone working on the more general solution of
> supporting a gzipped version of (almost) any Galaxy datatype?
> https://bitbucket.org/galaxy/galaxy-central/issue/666/

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[galaxy-dev] .gz extension gets stripped off when uploading via data library Upload via filesystem paths but not via Get Data -> Upload File

[Leandro Hermida]

Hello,

We've created a new binary datatype for .fastq.gz files following the
same methodology as the BAM files since we don't want our fasta.gz
files to be gunzipped.  I added the appropriate code in upload.py to
make sure of this.  This new datatype and extension successfully does
not gunzip our files.  But when we upload it into a data library via
the data library "Upload via filesystem paths" it for some reason
automatically strips the .gz part out. When we take the same .fastq.gz
file and upload it via Get Data -> Upload File it works fine, nothing
is stripped from file name. Where is it doing this and how can prevent
from stripping the .gz via the data library menus?

thanks,
Leandro
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[galaxy-dev] Galaxy Tool Shed used for main code hosting and collaborative development repo?

[Leandro Hermida]

Hi,

Quick question about the Galaxy Tool Shed, I would like to publish a tool
suite there and wondering to people use the tool shed repositories as their
main code hosting and development site or is it typical that people have
their code hosted somewhere else a la Github or Sourceforge?

regards,
Leandro
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[galaxy-dev] enabled user_library_import_dir but see nothing in the GUI to be able to create data libraries

[Leandro Hermida]

Hi all,

I've enabled the universe.wsgi feature user_library_import_dir feature
and made a sub-directory with my login and put some test files there.
I've also made myselfa  non-admin to test and after restart the Galaxy
server I see no where in the GUI where I can import data libraries??
Am I missing something?

regards,
Leandro
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[galaxy-dev] uploading binary files checksum changes, Galaxy doing something to file?

[Leandro Hermida]

Hi all,

We tried to find something in the docs and mailing list no luck.  We
created a new datatype the is a straight subclass of Binary and then
when we upload such a file in the Galaxy UI and check the checksums
between the original file and the file located in the Galaxy
database/files/... directory their checksums are different!

What are we doing wrong? We simply want Galaxy to upload and no touch
the file at all.

regards,
Leandro
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Re: [galaxy-dev] value_label tool input param attribute doesn't work as documented

[Leandro Hermida]

Hi again,

Sorry had to check what exactly was not working, the value_label
attribute appears to not work when trying to reference a label from a
dynamic_options driven input parameter.

regards,
Leandro

On Wed, Aug 24, 2011 at 7:23 PM, Kanwei Li  wrote:
> Hi Leandro,
> I tested this on my instance and the example you gave did give me the
> correct string: Human (hg18). Do you still have this problem? If so, can you
> provide an example where it still behaves incorrectly?
> Thanks,
> K
>
> On Thu, Jul 14, 2011 at 4:16 AM, Leandro Hermida
>  wrote:
>>
>> Hi,
>>
>> Looking at the example on the Tool Config Syntax wiki page:
>>
>> Example
>>
>> Assume that the tool includes an input parameter named "database" which is
>> a select list ( e.g., assume the following inputs ):
>>
>> Toggle line numbers
>>
>>1 
>>
>>
>>2 
>>
>>
>>3 
>>
>>
>>4 Human (hg18)
>>
>>
>>5 Fly (dm3)
>>
>>
>>6 
>>
>>
>>7 
>>
>>
>> Assume that the user selects the first option in the $database select
>> list. Then the following will ensure that the tool produces a tabular data
>> set whose associated history item has the label "Blat on Human (hg18)".
>>
>> Toggle line numbers
>>
>>1 
>>
>>
>>2 
>>
>>
>>3 
>>
>>
>>
>> It shows that .value_label attribute should produce the string in between
>> the  tags, not the actual value.
>>
>> Why does this not work? When I use it it produces the value, or am I doing
>> something wrong?
>>
>> regards,
>> Leandro
>>
>>
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[galaxy-dev] problems with two coupled select menus using dynamic_options and refresh_on_change

[Leandro Hermida]

Hi,

I am trying to create a form where there are two select menus, both using
dynamic_options, where one is the parent menu that is chosen first and based
on the selection(s) there is a refresh and the second menu gets populated
based on the first menu's choice(s).




There seems to be a problem when the form loads for the first time as $names
is not selected yet.  I get a syntax error like "Invalid string", when I
remove $names as a parameters from my second dynamic_options function call
everything is fine.  Does someone know how to achieve the functionality I'm
aiming for in Galaxy without having to use the deprecated  tags?  Is
there a way in Cheetah to set a default value for $names and if so how would
I do this in the tool xml?

regards,
Leandro
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[galaxy-dev] value_label tool input param attribute doesn't work as documented

[Leandro Hermida]

Hi,

Looking at the example on the Tool Config Syntax wiki page:
Example

Assume that the tool includes an input parameter named "database" which is a
select list ( e.g., assume the following inputs ):
Toggle line 
numbers

   1 


   2 


   3 


   4 

*Human (hg18)*
   5 

Fly (dm3)
   6 


   7 



Assume that the user selects the first option in the $database select list.
Then the following will ensure that the tool produces a tabular data set
whose associated history item has the label "Blat on *Human (hg18)*".
Toggle line 
numbers

   1 


   2 


   3 



It shows that .value_label attribute should produce the string in between
the  tags, not the actual value.

Why does this not work? When I use it it produces the value, or am I doing
something wrong?

regards,
Leandro
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Re: [galaxy-dev] Galaxy forgetting history and giving me new blank history

[Leandro Hermida]

Hi - you can ignore this message, I figured out what the problem was and it
was caused by a change in my front end authentication setup

On Fri, Jul 1, 2011 at 10:21 AM, Leandro Hermida  wrote:

> Having a very strange problem in the Galaxy web GUI that suddenly just
> started happening yesterday, getting very strange behavior in the
> history right panel.
>
> - Most of the time when I click on something in the GUI like to go to
> a tool page or to go to the Admin interface and come back suddenly
> Galaxy just replaces my current history and gives me a brand new
> history, its like it forgets what history I'm working with
> - In tool forms sometimes input data drop downs don't have anything in
> them even though there are datasets in my history that are of the
> right datatype.  Could be related to problem above where it thinks
> maybe I'm in a new blank history
>
> Anyone have this ever happen?
>
> regards,
> Leandro
>
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Re: [galaxy-dev] public datasets/histories with external auth

[Leandro Hermida]

Hi again,

I just realized that my setup is not going to work at all and does that
exact thing you just mentioned, even if you are logged in it will set the
REMOTE_USER to anonymous when you click on any /datasets URL.  This causes
some strange Galaxy history behavior!

oops,
Leandro

On Fri, Jul 1, 2011 at 10:36 AM, Leandro Hermida  wrote:

> Hi Shantanu,
>
> Thank you for your update,  I've done my config a little differently and it
> appears to work just the same.  The relevant part looks like this:
>
>
>## ActiveDirectory authentication and authorization
>AuthType Basic
>AuthBasicProvider ldap
>AuthName "R&D Galaxy Testing/QA Server"
>AuthLDAPURL "ldap://my.server.com:389/OU=Users &
> Workstations,DC=domain,DC=com?sAMAccountName?sub?(|(objectClass=person)(objectClass=group))"
>
># ...more AuthLDAP directives here...
>
>RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e
>
>
>
>Order Allow,Deny
>Allow from All
>Satisfy Any
>
>RequestHeader set REMOTE_USER "anonymous"
>
>
>## Static content and reverse proxy
>RewriteEngine On
>RewriteRule ^/static/style/(.*)
> /path/to/galaxy/galaxy_dist/static/june_2007_style/blue/$1 [L]
>RewriteRule ^/static/scripts/(.*)
> /path/to/galaxy/galaxy_dist/static/scripts/packed/$1 [L]
>RewriteRule ^/static/(.*) /path/to/galaxy/galaxy_dist/static/$1 [L]
>RewriteRule ^/favicon.ico /path/to/galaxy/galaxy_dist/static/favicon.ico
> [L]
>RewriteRule ^/robots.txt /path/to/galaxy/galaxy_dist/static/robots.txt
> [L]
>RewriteRule ^(.*) http://galaxy.server.hostname:8080 [P]
>
>
>
>
> On Fri, Jul 1, 2011 at 12:13 AM, Shantanu Pavgi  wrote:
> >
> > On Jun 30, 2011, at 6:34 AM, Leandro Hermida wrote:
> >
> >> Hi Nate and Shantanu,
> >>
> >> Thanks so much for the clear guidance, this works and sorry I didn't
> >> read the Apache docs properly
> >>
> >> best,
> >> Leandro
> >>
> >> On Thu, Jun 30, 2011 at 6:14 AM, Shantanu Pavgi  wrote:
> >>>
> >>> On Jun 29, 2011, at 12:21 PM, Nate Coraor wrote:
> >>>
> >>> Leandro Hermida wrote:
> >>>
> >>> Hi Shantanu,
> >>>
> >>> In your Apache configuration exactly how did you set up an anonymous
> >>>
> >>> REMOTE_USER just for specific locations like the /datasets/ path?  I'm
> just
> >>>
> >>> looking at the Apache docs and the RequestHeader directive has a
> context of
> >>>
> >>> the entire VirtualHost and cannot be put into a Location container so
> I'm
> >>>
> >>> not sure how to do it.
> >>>
> >>> Hi Leandro,
> >>>
> >>> See the optional 'env=' argument and docs on the same for ways to make
> >>> RequestHeader conditional:
> >>>
> >>>
> http://httpd.apache.org/docs/current/mod/mod_headers.html#requestheader
> >>>
> >>> So, depending on the path accessed, you should be able to have
> >>> mod_rewrite set an environment variable specifying which REMOTE_USER
> >>> (real username or fake anonymouse user) should be set.
> >>>
> >>> You could also just set it as the anonymous user to start with and then
> >>> use 'RequestHeader set' to overwrite it with the real username in the
> >>> case that a real username is available.
> >>>
> >>> This is all just from glancing at the docs, though, I have not tried
> any
> >>> of it out, and this sort of Apache trickery is always difficult to get
> >>> right.
> >>>
> >>> --nate
> >>>
> >>>
> >>>
> >>> Leandro,
> >>> The RequestHeader has a context of 'directory' as well, which includes
> >>> , , , and  containers [1]. So you
> should
> >>> be able to use it in Location directive.
> >>> Following is a configuration snippet related to what Nate described in
> his
> >>> earlier response. We are setting REMOTE_USER variable to anonymous when
> it's
> >>> not set/empty.
> >>> 
> >>> AuthType shibboleth
> >>> ShibRequireSession off
> >>> Require shibboleth
> >>> RewriteCond %{LA-U:REMOTE_USER} =""
> >>>   

Re: [galaxy-dev] public datasets/histories with external auth

[Leandro Hermida]

Hi Shantanu,

Thank you for your update,  I've done my config a little differently and it
appears to work just the same.  The relevant part looks like this:

   
   ## ActiveDirectory authentication and authorization
   AuthType Basic
   AuthBasicProvider ldap
   AuthName "R&D Galaxy Testing/QA Server"
   AuthLDAPURL "ldap://my.server.com:389/OU=Users &
Workstations,DC=domain,DC=com?sAMAccountName?sub?(|(objectClass=person)(objectClass=group))"

   # ...more AuthLDAP directives here...

   RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e
   

   
   Order Allow,Deny
   Allow from All
   Satisfy Any
   RequestHeader set REMOTE_USER "anonymous"
   

   ## Static content and reverse proxy
   RewriteEngine On
   RewriteRule ^/static/style/(.*)
/path/to/galaxy/galaxy_dist/static/june_2007_style/blue/$1 [L]
   RewriteRule ^/static/scripts/(.*)
/path/to/galaxy/galaxy_dist/static/scripts/packed/$1 [L]
   RewriteRule ^/static/(.*) /path/to/galaxy/galaxy_dist/static/$1 [L]
   RewriteRule ^/favicon.ico /path/to/galaxy/galaxy_dist/static/favicon.ico
[L]
   RewriteRule ^/robots.txt /path/to/galaxy/galaxy_dist/static/robots.txt
[L]
   RewriteRule ^(.*) http://galaxy.server.hostname:8080 [P]



On Fri, Jul 1, 2011 at 12:13 AM, Shantanu Pavgi  wrote:
>
> On Jun 30, 2011, at 6:34 AM, Leandro Hermida wrote:
>
>> Hi Nate and Shantanu,
>>
>> Thanks so much for the clear guidance, this works and sorry I didn't
>> read the Apache docs properly
>>
>> best,
>> Leandro
>>
>> On Thu, Jun 30, 2011 at 6:14 AM, Shantanu Pavgi  wrote:
>>>
>>> On Jun 29, 2011, at 12:21 PM, Nate Coraor wrote:
>>>
>>> Leandro Hermida wrote:
>>>
>>> Hi Shantanu,
>>>
>>> In your Apache configuration exactly how did you set up an anonymous
>>>
>>> REMOTE_USER just for specific locations like the /datasets/ path?  I'm
just
>>>
>>> looking at the Apache docs and the RequestHeader directive has a context
of
>>>
>>> the entire VirtualHost and cannot be put into a Location container so
I'm
>>>
>>> not sure how to do it.
>>>
>>> Hi Leandro,
>>>
>>> See the optional 'env=' argument and docs on the same for ways to make
>>> RequestHeader conditional:
>>>
>>>
http://httpd.apache.org/docs/current/mod/mod_headers.html#requestheader
>>>
>>> So, depending on the path accessed, you should be able to have
>>> mod_rewrite set an environment variable specifying which REMOTE_USER
>>> (real username or fake anonymouse user) should be set.
>>>
>>> You could also just set it as the anonymous user to start with and then
>>> use 'RequestHeader set' to overwrite it with the real username in the
>>> case that a real username is available.
>>>
>>> This is all just from glancing at the docs, though, I have not tried any
>>> of it out, and this sort of Apache trickery is always difficult to get
>>> right.
>>>
>>> --nate
>>>
>>>
>>>
>>> Leandro,
>>> The RequestHeader has a context of 'directory' as well, which includes
>>> , , , and  containers [1]. So you
should
>>> be able to use it in Location directive.
>>> Following is a configuration snippet related to what Nate described in
his
>>> earlier response. We are setting REMOTE_USER variable to anonymous when
it's
>>> not set/empty.
>>> 
>>> AuthType shibboleth
>>> ShibRequireSession off
>>> Require shibboleth
>>> RewriteCond %{LA-U:REMOTE_USER} =""
>>> RequestHeader set REMOTE_USER "anonymous"
>>> 
>>> Hope this helps.
>>>
>>> 1. http://httpd.apache.org/docs/current/mod/directive-dict.html#Context
>>> --
>>> Shantanu.
>>>
>
>
> Leandro,
>
> I realized that above mentioned configuration is wrong. It will set
RequestHeader to 'anonymous' regardless of authentication status. I think
following config should work (still testing). In our case it resides outside
of Location directive now. You may need to adjust it according to your
setup:
>
> {{{
># Take the  environment variable and set it as a header in the
proxy request.
>RewriteCond %{IS_SUBREQ} ^false$
>RewriteCond %{LA-U:REMOTE_USER} (.+)
>RewriteRule . - [E=RU:%1]
># Set RU to anonymous if No REMOTE_USER
>RewriteCond %{IS_SUBREQ} ^false$
>RewriteCond %{LA-U:REMOTE_USER} =""
>RewriteRule . - [E=RU:"anonymous"]
># Set RequestHeader
>RequestHeader set REMOTE_USER %{RU}e
> }}}
>
>
> --
> Shantanu.
>
>
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[galaxy-dev] Galaxy forgetting history and giving me new blank history

[Leandro Hermida]

Having a very strange problem in the Galaxy web GUI that suddenly just
started happening yesterday, getting very strange behavior in the
history right panel.

- Most of the time when I click on something in the GUI like to go to
a tool page or to go to the Admin interface and come back suddenly
Galaxy just replaces my current history and gives me a brand new
history, its like it forgets what history I'm working with
- In tool forms sometimes input data drop downs don't have anything in
them even though there are datasets in my history that are of the
right datatype.  Could be related to problem above where it thinks
maybe I'm in a new blank history

Anyone have this ever happen?

regards,
Leandro
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Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple="true" input datasets

[Leandro Hermida]

Hi Kip,

For the time being we are using this method to achieve the same
result, although its not as nice as just having a multi-select menu in
the form:


...
$input1
#for $r in $add_inputs
$r.$input2
#end for
...


In :







best,
Leandro


On Thu, Jun 30, 2011 at 4:52 PM, Kip Bodi  wrote:
> Sorry, I tried to edit that, to make it simpler, but missed the 
> block. The 'name' does match the one in the 'command' on my end
> (list_of_items_in_history).
>
> On Thu, Jun 30, 2011 at 10:45 AM, Kip Bodi  wrote:
>>
>> Hi all,
>>
>> I'm having the same problem. I have a script that tries to take several
>> history data sets as a single input:
>>
>> aggregate.pl --out $outfile
>> $list_of_items_in_history
>>
>>   
>>     > label="Fitness score table, per site"/>
>>   
>>
>>   
>>     
>>   
>>
>> If I select only one history item it works, but if I press 'ctrl' to
>> select multiple items, it fails:
>>
>> File
>> '/storage/apps/galaxy_dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
>> line 364 in respond
>>   app_iter = self.application(environ, detect_start_response)
>> File '/usr/lib/python2.6/site-packages/paste/debug/prints.py', line 106 in
>> __call__
>>   environ, self.app)
>> File '/usr/lib/python2.6/site-packages/paste/wsgilib.py', line 543 in
>> intercept_output
>>   app_iter = application(environ, replacement_start_response)
>> File '/usr/lib/python2.6/site-packages/paste/recursive.py', line 80 in
>> __call__
>>   return self.application(environ, start_response)
>> File '/usr/lib/python2.6/site-packages/paste/httpexceptions.py', line 633
>> in __call__
>>   return self.application(environ, start_response)
>> File '/storage/apps/galaxy_dist/lib/galaxy/web/framework/base.py', line
>> 145 in __call__
>>   body = method( trans, **kwargs )
>> File
>> '/storage/apps/galaxy_dist/lib/galaxy/web/controllers/tool_runner.py', line
>> 68 in index
>>   template, vars = tool.handle_input( trans, params.__dict__ )
>> File '/storage/apps/galaxy_dist/lib/galaxy/tools/__init__.py', line 979 in
>> handle_input
>>   _, out_data = self.execute( trans, incoming=params, history=history )
>> File '/storage/apps/galaxy_dist/lib/galaxy/tools/__init__.py', line 1271
>> in execute
>>   return self.tool_action.execute( self, trans, incoming=incoming,
>> set_output_hid=set_output_hid, history=history, **kwargs )
>> File '/storage/apps/galaxy_dist/lib/galaxy/tools/actions/__init__.py',
>> line 360 in execute
>>   for name, value in tool.params_to_strings( incoming, trans.app
>> ).iteritems():
>> File '/storage/apps/galaxy_dist/lib/galaxy/tools/__init__.py', line 1274
>> in params_to_strings
>>   return params_to_strings( self.inputs, params, app )
>> File '/storage/apps/galaxy_dist/lib/galaxy/tools/parameters/__init__.py',
>> line 79 in params_to_strings
>>   value = params[ key ].value_to_basic( value, app )
>> File '/storage/apps/galaxy_dist/lib/galaxy/tools/parameters/basic.py',
>> line 110 in value_to_basic
>>   return self.to_string( value, app )
>> File '/storage/apps/galaxy_dist/lib/galaxy/tools/parameters/basic.py',
>> line 1457 in to_string
>>   return value.id
>> AttributeError: 'list' object has no attribute 'id'
>>
>> Is using multiple history items as a single input not currently supported,
>> or is there something else I'm doing wrong?
>>
>> Cheers,
>>
>> Kip
>>
>> On Thu, Jun 9, 2011 at 7:05 AM, Leandro Hermida
>>  wrote:
>>>
>>> Hi again,
>>>
>>> Sorry to ping again about this, just very interested in knowing if
>>> this is a missing feature in Galaxy or if I had configured something
>>> wrong.
>>>
>>> Is it possible in Galaxy to have a tool with a multiple="true" input
>>> dataset parameter?  It doesn't seem so?
>>>
>>> best,
>>> Leandro
>>>
>>>
>>> On Tue, May 24, 2011 at 1:31 PM, Leandro Hermida
>>>  wrote:
>>> > Hi Nate,
>>> >
>>> > Thanks for the ping, have fun at the conference!
>>> > On Tue, May 24, 2011 at 11:22 AM, Nate Coraor  wrote:
>>> >>
>>> >> Hi Leandro,
>>> >>
>>> >> The Galaxy Team has recently been p

Re: [galaxy-dev] public datasets/histories with external auth

[Leandro Hermida]

Hi Nate and Shantanu,

Thanks so much for the clear guidance, this works and sorry I didn't
read the Apache docs properly

best,
Leandro

On Thu, Jun 30, 2011 at 6:14 AM, Shantanu Pavgi  wrote:
>
> On Jun 29, 2011, at 12:21 PM, Nate Coraor wrote:
>
> Leandro Hermida wrote:
>
> Hi Shantanu,
>
> In your Apache configuration exactly how did you set up an anonymous
>
> REMOTE_USER just for specific locations like the /datasets/ path?  I'm just
>
> looking at the Apache docs and the RequestHeader directive has a context of
>
> the entire VirtualHost and cannot be put into a Location container so I'm
>
> not sure how to do it.
>
> Hi Leandro,
>
> See the optional 'env=' argument and docs on the same for ways to make
> RequestHeader conditional:
>
>    http://httpd.apache.org/docs/current/mod/mod_headers.html#requestheader
>
> So, depending on the path accessed, you should be able to have
> mod_rewrite set an environment variable specifying which REMOTE_USER
> (real username or fake anonymouse user) should be set.
>
> You could also just set it as the anonymous user to start with and then
> use 'RequestHeader set' to overwrite it with the real username in the
> case that a real username is available.
>
> This is all just from glancing at the docs, though, I have not tried any
> of it out, and this sort of Apache trickery is always difficult to get
> right.
>
> --nate
>
>
>
> Leandro,
> The RequestHeader has a context of 'directory' as well, which includes
> , , , and  containers [1]. So you should
> be able to use it in Location directive.
> Following is a configuration snippet related to what Nate described in his
> earlier response. We are setting REMOTE_USER variable to anonymous when it's
> not set/empty.
>         
>                 AuthType shibboleth
>                 ShibRequireSession off
>                 Require shibboleth
>                 RewriteCond %{LA-U:REMOTE_USER} =""
>                 RequestHeader set REMOTE_USER "anonymous"
>         
> Hope this helps.
>
> 1. http://httpd.apache.org/docs/current/mod/directive-dict.html#Context
> --
> Shantanu.
>

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Re: [galaxy-dev] public datasets/histories with external auth

[Leandro Hermida]

Hi Shantanu,

In your Apache configuration exactly how did you set up an anonymous
REMOTE_USER just for specific locations like the /datasets/ path?  I'm just
looking at the Apache docs and the RequestHeader directive has a context of
the entire VirtualHost and cannot be put into a Location container so I'm
not sure how to do it.

thanks,
Leandro

On Wed, Jun 22, 2011 at 9:40 PM, Shantanu Pavgi  wrote:

>
> On Jun 20, 2011, at 4:10 PM, Shantanu Pavgi wrote:
>
> >
> > On Jun 20, 2011, at 2:40 PM, Nate Coraor wrote:
> >
> >> Shantanu Pavgi wrote:
> >>> Hi,
> >>>
> >>> We have a galaxy server setup using external shibboleth authentication.
> While we would like to have site behind authentication realm, there are
> instances when our galaxy datasets/histories need to be accessible publicly
> from other websites. We tried adding an exception to auth rule for /datasets
>  path using Location directive in apache web server configuration, however
> galaxy server returned an error as:
> >>>
> >>> {{{
> >>> Access to Galaxy is denied
> >>> Galaxy is configured to authenticate users via an external method (such
> as HTTP authentication in Apache), but a username was not provided by the
> upstream (proxy) server. This is generally due to a misconfiguration in the
> upstream server.
> >>> }}}
> >>>
> >>> Is there any way to share public histories and datasets when galaxy is
> using external authentication mechanism? I have thought about setting up
> (fake) anonymous REMOTE_USER variable for /datasets path, but  not sure
> whether this is correct approach. Also, would it require any galaxy code
> changes? Any thoughts?
> >>
> >> Hi Shantanu,
> >>
> >> That's about all you can do, or modify
> >> lib/galaxy/web/framework/middleware/remoteuser.py to let these
> >> connections through.  I would suggest the former solution of setting a
> >> header in Apache, but only set it if the user is not authenticated.
> >>
> >> --nate
> >
> >
> > Thanks for the reply Nate. That's helpful.
> >
> > --
> > Shantanu.
> >
>
>
> I did a test by excluding following URLs from Apache-Shibboleth external
> authentication and it seems to be working:
> -  /datasets/
> -  /u//h/
> - /static/  (css and javascript)
>
> Do I need to exclude any other URLs so that published histories and
> datasets can be accessed from remote sites without authentication? Also,
> will it offer read-only access to the galaxy interface? Does it expose any
> job submission, file-uploads or any other modification/execution operations
> using web interface?
>
> Also, can we prevent particular galaxy-user from carrying out certain
> actions, e.g. running jobs, file uploads etc.? Since galaxy will create
> 'anonymous' user account based on the REMOTE_USER variable set for
> unauthenticated requests, I am wondering if such locked-down mode will be
> possible for a particular galaxy-user.
>
>
> Thanks,
> Shantanu.
>
>
>
>
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[galaxy-dev] updating ToolsMultipleOutput wiki docs new additional datasets file format to include database part

[Leandro Hermida]

Hi,

In the last section of
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput,
"Number of output datasets cannot be determined until tool run", it should
be updated that the new additional datasets file format actually has a sixth
part at the end where you can set the database attribute of the output
dataset:

"%s_%s_%s_%s_%s_%s" % ( 'primary', output1.id, name, 'visible', file_type,
database )

I accidentally discovered this even though I didn't want to set the database
attribute because I have some custom datatypes defined and my datatype
extension names have underscores in them :) which causes Galaxy to think
that the part of my extension names string after the underscore is actually
the database name i want to set.

I would recommend not to put underscores in your custom datatype extension
names :)

-Leandro
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Re: [galaxy-dev] change dataset label in exec_after_process()

[Leandro Hermida]

Hi Ross,

I agree, normally I use the label="" xml tag when possible, but the reason I
ask this question is because I have a tool where the number of output
datasets cannot be determined until the tool is run (a la
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput) and I
really would like to change the dataset labels/names of what is produced.

Could you provide some insight as to how you get it to work with one of the
hooks? You might have seen in another post I made yesterday, when I try even
just a simple example using exec_before_job() I get some strange error :-/

thanks again,
leandro

On Fri, Jun 24, 2011 at 10:09 AM, Ross  wrote:

> I used to use the post job hook but I think it's a lot cleaner to use
> the label option - eg where I want the output name based on a user
> supplied text string "out_prefix", something like:
>
>  
>
>  
>
> works for me and avoids the need to have a post execution hook code file.
>
> On Fri, Jun 24, 2011 at 6:02 PM, Leandro Hermida
>  wrote:
> > Hi again,
> >
> > Sorry that I didn't know before, it seems like the label is the the
> object
> > attribute 'name' programmatically, but even if I set this in
> > exec_before_job(), exec_before_process(), exec_after_process() it doesn't
> > change the dataset name even after refreshing my history.
> >
> > Has anyone had success setting dataset label/name and other attributes
> using
> > one of the custom code hook functions??
> >
>
>
> --
> Ross Lazarus MBBS MPH;
> Associate Professor, Harvard Medical School;
> Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
>
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Re: [galaxy-dev] change dataset label in exec_after_process()

[Leandro Hermida]

Hi again,

Sorry that I didn't know before, it seems like the label is the the object
attribute 'name' programmatically, but even if I set this in
exec_before_job(), exec_before_process(), exec_after_process() it doesn't
change the dataset name even after refreshing my history.

Has anyone had success setting dataset label/name and other attributes using
one of the custom code hook functions??

thanks,
leandro

On Thu, Jun 23, 2011 at 3:27 PM, Leandro Hermida  wrote:

> Hi everyone,
>
> Is it possible to change dataset labels in exec_after_process() ?
>
> best,
> Leandro
>
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[galaxy-dev] error when using exec_before_job

[Leandro Hermida]

Hi,

I've tried to do a simple test where I change the output dataset name
programmatically before it appears in the history using exec_before_job().
I just copied some example code:

def exec_before_job(inp_data, out_data, param_dict, tool):
for name, data in out_data.items():
data.name = 'New name'

I get the following error:

Traceback (most recent call last):
  File 
"/gpfshpc/home/lhermida/soft/galaxy/galaxy_dist/lib/galaxy/jobs/runners/drmaa.py",
line 124, in queue_job
job_wrapper.prepare()
  File 
"/gpfshpc/home/lhermida/soft/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py",
line 364, in prepare
out_data=out_data, tool=self.tool, param_dict=incoming)
  File 
"/gpfshpc/home/lhermida/soft/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py",
line 1664, in call_hook
return code( *args, **kwargs )
TypeError: ('E', 'r', 'r', 'o', 'r', ' ', 'i', 'n', ' ', "'", 'T',
'e', 's', 't', 'i', 'n', 'g', "'", ' ', 'h', 'o', 'o', 'k', ' ', "'",
'e', 'x', 'e', 'c', '_', 'b', 'e', 'f', 'o', 'r', 'e', '_', 'j', 'o',
'b', "'", ',', ' ', 'o', 'r', 'i', 'g', 'i', 'n', 'a', 'l', ' ', 'm',
'e', 's', 's', 'a', 'g', 'e', ':', ' ', 'e', 'x', 'e', 'c', '_', 'b',
'e', 'f', 'o', 'r', 'e', '_', 'j', 'o', 'b', '(', ')', ' ', 'g', 'o',
't', ' ', 'm', 'u', 'l', 't', 'i', 'p', 'l', 'e', ' ', 'v', 'a', 'l',
'u', 'e', 's', ' ', 'f', 'o', 'r', ' ', 'k', 'e', 'y', 'w', 'o', 'r',
'd', ' ', 'a', 'r', 'g', 'u', 'm', 'e', 'n', 't', ' ', "'", 'i', 'n',
'p', '_', 'd', 'a', 't', 'a', "'")


Any ideas?
Leandro
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[galaxy-dev] change dataset label in exec_after_process()

[Leandro Hermida]

Hi everyone,

Is it possible to change dataset labels in exec_after_process() ?

best,
Leandro
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Re: [galaxy-dev] use external authentication bare username as email address without appending any email domain

[Leandro Hermida]

Hi again,

Commenting out the following if-then-else as Nate recommended works in
remoteuser.py works to achieve this goal:

#if not environ[ 'HTTP_REMOTE_USER' ].count( '@' ):
#if self.maildomain is not None:
#environ[ 'HTTP_REMOTE_USER' ] += '@' + self.maildomain
#else:
#title = "Access to Galaxy is denied"
#message = """
#Galaxy is configured to authenticate users
via an external
#method (such as HTTP authentication in
Apache), but only a
#username (not an email address) was provided by the
#upstream (proxy) server.  Since Galaxy
usernames are email
#addresses, a default mail domain must be set.
#   Please contact your local Galaxy administrator.  The
#variable remote_user_maildomain
must be set
#before you may access Galaxy.
#"""
#return self.error( start_response, title, message )

So far in regular Galaxy use everything works no problem, people's
email addresses are their usernames and email services work in Windows
as your username is your email nickname.

-L

On Thu, Jun 9, 2011 at 11:00 PM, Leandro Hermida
 wrote:
> Hi Nate,
>
> Thank so much for the instructions :) , yes this is what I would want
> to do as Galaxy was adding an empty @ after the username.  Yep in a
> Windows domain environment the bare username (sAMAccountName) is also
> an email nickname and works with the Exchange server when you use SMTP
> services.
>
> thank a lot,
> Leandro
>
> On Thu, Jun 9, 2011 at 6:54 PM, Nate Coraor  wrote:
>> Leandro Hermida wrote:
>>> Hi,
>>>
>>> Is it possible to tell Galaxy to use the bare username passed back by
>>> external authentication as the email address without appending any
>>> domain?  It seems to complain if it isn't in email address format and
>>> asks you to set up a domain to append in universe.wsgi.
>>>
>>> I would like to use the bare username as the email address since it
>>> works fine as an email address in for example any Active
>>> Directory-based organization and also in many non-academic
>>> organizations it is preferred not to use the email addresses as the
>>> ID.
>>
>> Hi Leandro,
>>
>> If you're using any of Galaxy's mail services, your SMTP server would
>> also need to be able to accept mail to users with no domain.  That said,
>> you should be able to hack
>> lib/galaxy/web/framework/middleware/remoteuser.py to do what you want.
>>
>> Specifically, remove/comment the conditional:
>>
>>  if not environ[ 'HTTP_REMOTE_USER' ].count( '@' ):
>>
>> --nate
>>
>>>
>>> thanks in advance,
>>> Leandro
>>> ___
>>> 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/
>>
>

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Re: [galaxy-dev] use external authentication bare username as email address without appending any email domain

[Leandro Hermida]

Hi Nate,

Thank so much for the instructions :) , yes this is what I would want
to do as Galaxy was adding an empty @ after the username.  Yep in a
Windows domain environment the bare username (sAMAccountName) is also
an email nickname and works with the Exchange server when you use SMTP
services.

thank a lot,
Leandro

On Thu, Jun 9, 2011 at 6:54 PM, Nate Coraor  wrote:
> Leandro Hermida wrote:
>> Hi,
>>
>> Is it possible to tell Galaxy to use the bare username passed back by
>> external authentication as the email address without appending any
>> domain?  It seems to complain if it isn't in email address format and
>> asks you to set up a domain to append in universe.wsgi.
>>
>> I would like to use the bare username as the email address since it
>> works fine as an email address in for example any Active
>> Directory-based organization and also in many non-academic
>> organizations it is preferred not to use the email addresses as the
>> ID.
>
> Hi Leandro,
>
> If you're using any of Galaxy's mail services, your SMTP server would
> also need to be able to accept mail to users with no domain.  That said,
> you should be able to hack
> lib/galaxy/web/framework/middleware/remoteuser.py to do what you want.
>
> Specifically, remove/comment the conditional:
>
>  if not environ[ 'HTTP_REMOTE_USER' ].count( '@' ):
>
> --nate
>
>>
>> thanks in advance,
>> Leandro
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>>   http://lists.bx.psu.edu/
>

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Re: [galaxy-dev] select menu in conditional tag cannot be set at runtime in workflow editor

[Leandro Hermida]

Also want to ping again about this possible bug or feature.

-Leandro

On Fri, May 13, 2011 at 2:57 PM, Leandro Hermida
 wrote:
> Hi all,
>
> In a tool XML I have a select menu param within/driving a conditional tag
> and in the workflow editor it doesn't let me choose to allow the user to set
> this select menu at runtime?  Is this a bug?
>
> best,
> leandro
>
>

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Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple="true" input datasets

[Leandro Hermida]

Hi again,

Sorry to ping again about this, just very interested in knowing if
this is a missing feature in Galaxy or if I had configured something
wrong.

Is it possible in Galaxy to have a tool with a multiple="true" input
dataset parameter?  It doesn't seem so?

best,
Leandro


On Tue, May 24, 2011 at 1:31 PM, Leandro Hermida
 wrote:
> Hi Nate,
>
> Thanks for the ping, have fun at the conference!
> On Tue, May 24, 2011 at 11:22 AM, Nate Coraor  wrote:
>>
>> Hi Leandro,
>>
>> The Galaxy Team has recently been preparing for and traveling in advance
>> of the Galaxy Community Conference, which begins today.  Unfortunately I
>> don't have an answer for you, but when we're all back at work next week,
>> someone should be able to respond.
>>
>> Thanks,
>> --nate
>>
>> Leandro Hermida wrote:
>> > Hi again,
>> >
>> > Very sorry to ask again, just gotten no repsonse, but is this a Galaxy
>> > bug
>> > or does anyone have a functioning tool that takes multiple datasets as
>> > an
>> > input parameter??? i.e.
>> >
>> > 
>> >
>> > regards,
>> > Leandro
>> >
>> > On Thu, May 19, 2011 at 7:15 PM, Leandro Hermida
>> > > > > wrote:
>> >
>> > > Hi again,
>> > >
>> > > I tried changing the format to txt and tabular which I have other
>> > > datasets
>> > > in my history and still the same error and stack trace in Galaxy.
>> > >
>> > > Is it possible at all to have a select multiple of datasets as an
>> > > input
>> > > parameter??
>> > >
>> > > best,
>> > > Leandro
>> > >
>> > >
>> > > On Thu, May 19, 2011 at 6:59 PM, Leandro Hermida <
>> > > soft...@leandrohermida.com> wrote:
>> > >
>> > >> Hi Galaxy developers,
>> > >>
>> > >> Something seems maybe to be wrong with the format="html" type... I
>> > >> forgot
>> > >> to add before that my tool input param the format="html" attribute:
>> > >>
>> > >> 
>> > >>
>> > >> In another tool I have it outputs format="html" and this works and
>> > >> displays in Galaxy just fine. I would like to use multiple of these
>> > >> output
>> > >> datasets in my history as the input for this other tool but something
>> > >> seems
>> > >> to be wrong if you try to do this?
>> > >>
>> > >> a bit lost,
>> > >> Leandro
>> > >>
>> > >>
>> > >> On Thu, May 19, 2011 at 3:30 PM, Leandro Hermida <
>> > >> soft...@leandrohermida.com> wrote:
>> > >>
>> > >>> Hi,
>> > >>>
>> > >>> I have a tool where the input is multi-select of datasets, e.g.:
>> > >>>
>> > >>> 
>> > >>>
>> > >>> I tested it to see what it would pass to my command and I get the
>> > >>> following debug page and error in Galaxy:
>> > >>>
>> > >>> AttributeError: 'list' object has no attribute 'missing_meta'
>> > >>>
>> > >>> The last part of the stack trace looks like:
>> > >>>
>> > >>> >>  validator.validate( value, history )
>> > >>> Module galaxy.tools.parameters.validation:185 in validate
>> > >>>
>> > >>> history 
>> > >>> self        > > >>> object
>> > >>> at 0xb8e6250>
>> > >>> value [,
>> > >>> ]
>> > >>>
>> > >>> >>  if value and value.missing_meta( check = self.check, skip =
>> > >>> >> self.skip
>> > >>> ):
>> > >>> AttributeError: 'list' object has no attribute 'missing_meta'
>> > >>>
>> > >>> What am I doing wrong?
>> > >>>
>> > >>> regards,
>> > >>> Leandro
>> > >>>
>> > >>>
>> > >>
>> > >
>>
>> > ___
>> > 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/
>>
>
>

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[galaxy-dev] use external authentication bare username as email address without appending any email domain

[Leandro Hermida]

Hi,

Is it possible to tell Galaxy to use the bare username passed back by
external authentication as the email address without appending any
domain?  It seems to complain if it isn't in email address format and
asks you to set up a domain to append in universe.wsgi.

I would like to use the bare username as the email address since it
works fine as an email address in for example any Active
Directory-based organization and also in many non-academic
organizations it is preferred not to use the email addresses as the
ID.

thanks in advance,
Leandro
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[galaxy-dev] new galaxy-dist fixes multiple IE UI bugs

[Leandro Hermida]

Thanks Galaxy Dev Team, the new galaxy-dist fixes multiple UI bugs with IE,
for e.g. the workflow editor works now works and the history expand/collapse
works! :)
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Re: [galaxy-dev] galaxy download

[Leandro Hermida]

See this page for the official installation instructions

https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy


2011/5/24 Björn Grüning 

> Hi Jasmin,
>
> at first you need to install mercurial. Under debian/ubuntu install it
> with:
>
> sudo apt-get mercurial
>
> Then you can check out all the necessary stuff with:
>
> hg clone https://bitbucket.org/galaxy/galaxy-dist
>
> You can start galaxy with:
>
> ./run.sh
>
> For more information, please see the wiki page.
> https://bitbucket.org/galaxy/galaxy-central/wiki/Home
>
> Ciao,
> Bjoern
>
>
> Am Dienstag, den 24.05.2011, 08:21 +0300 schrieb jasmine jacob:
> > Hi, I am a new linux user, would like to use  galaxy directly on my
> > computer could you instruct me how to download galaxy?
> >
> > thanks
> >
> > Jasmine Jacob-Hirsch
> > Functional Genomics
> > Cancer Research Center
> > Sheba Medical Center
> > 972-3-5302147
> > 972-523790500
> >
> >
> > ___
> > 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/
>
> --
> Björn Grüning
> Albert-Ludwigs-Universität Freiburg
> Institut für Pharmazeutische Wissenschaften
> Pharmazeutische Bioinformatik
> Hermann-Herder-Strasse 9
> D-79104 Freiburg i. Br.
>
> Tel.:  +49 761 203-4872
> Fax.:  +49 761 203-6366
> E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
> Web: http://www.pharmaceutical-bioinformatics.org/
>
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>
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Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple="true" input datasets

[Leandro Hermida]

Hi Nate,

Thanks for the ping, have fun at the conference!
On Tue, May 24, 2011 at 11:22 AM, Nate Coraor  wrote:

> Hi Leandro,
>
> The Galaxy Team has recently been preparing for and traveling in advance
> of the Galaxy Community Conference, which begins today.  Unfortunately I
> don't have an answer for you, but when we're all back at work next week,
> someone should be able to respond.
>
> Thanks,
> --nate
>
> Leandro Hermida wrote:
> > Hi again,
> >
> > Very sorry to ask again, just gotten no repsonse, but is this a Galaxy
> bug
> > or does anyone have a functioning tool that takes multiple datasets as an
> > input parameter??? i.e.
> >
> > 
> >
> > regards,
> > Leandro
> >
> > On Thu, May 19, 2011 at 7:15 PM, Leandro Hermida <
> soft...@leandrohermida.com
> > > wrote:
> >
> > > Hi again,
> > >
> > > I tried changing the format to txt and tabular which I have other
> datasets
> > > in my history and still the same error and stack trace in Galaxy.
> > >
> > > Is it possible at all to have a select multiple of datasets as an input
> > > parameter??
> > >
> > > best,
> > > Leandro
> > >
> > >
> > > On Thu, May 19, 2011 at 6:59 PM, Leandro Hermida <
> > > soft...@leandrohermida.com> wrote:
> > >
> > >> Hi Galaxy developers,
> > >>
> > >> Something seems maybe to be wrong with the format="html" type... I
> forgot
> > >> to add before that my tool input param the format="html" attribute:
> > >>
> > >> 
> > >>
> > >> In another tool I have it outputs format="html" and this works and
> > >> displays in Galaxy just fine. I would like to use multiple of these
> output
> > >> datasets in my history as the input for this other tool but something
> seems
> > >> to be wrong if you try to do this?
> > >>
> > >> a bit lost,
> > >> Leandro
> > >>
> > >>
> > >> On Thu, May 19, 2011 at 3:30 PM, Leandro Hermida <
> > >> soft...@leandrohermida.com> wrote:
> > >>
> > >>> Hi,
> > >>>
> > >>> I have a tool where the input is multi-select of datasets, e.g.:
> > >>>
> > >>> 
> > >>>
> > >>> I tested it to see what it would pass to my command and I get the
> > >>> following debug page and error in Galaxy:
> > >>>
> > >>> AttributeError: 'list' object has no attribute 'missing_meta'
> > >>>
> > >>> The last part of the stack trace looks like:
> > >>>
> > >>> >>  validator.validate( value, history )
> > >>> Module galaxy.tools.parameters.validation:185 in validate
> > >>>
> > >>> history 
> > >>> self object
> > >>> at 0xb8e6250>
> > >>> value [,
> > >>> ]
> > >>>
> > >>> >>  if value and value.missing_meta( check = self.check, skip =
> self.skip
> > >>> ):
> > >>> AttributeError: 'list' object has no attribute 'missing_meta'
> > >>>
> > >>> What am I doing wrong?
> > >>>
> > >>> regards,
> > >>> Leandro
> > >>>
> > >>>
> > >>
> > >
>
>  > ___
> > 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/
>
>
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Re: [galaxy-dev] nice quality Galaxy logo and name

[Leandro Hermida]

Hi Dave, thank you much appreciated!

On Tue, May 24, 2011 at 9:43 AM, Dave Clements
wrote:

> Hi Leandro,
>
> I apologize for the delay in answering this.
>
> The highest resolution logo I have is at
> http://gmod.org/wiki/File:GalaxyLogoBigger.png, which may not be big
> enough for some purposes, but will look much better than what you have been
> using.
>
> Sometime in the near future I hope to get a page like this
> http://gmod.org/wiki/GMOD_Promotion up for Galaxy.
>
> Thanks,
>
> Dave C.
>
>   On Thu, May 19, 2011 at 12:15 PM, Leandro Hermida <
> soft...@leandrohermida.com> wrote:
>
>>  Hi there,
>>
>> Would anyone have a nice quality Galaxy logo and name image for
>> presentations and posters?  I've been using the one in the left hand corner
>> of the server which ok but wondering if there is a better official one or
>> something
>>
>> regards,
>> leandro
>>
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>>  http://lists.bx.psu.edu/
>>
>
>
>
> --
> http://galaxy.psu.edu/gcc2011/
> http://getgalaxy.org
> http://usegalaxy.org/
>
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Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple="true" input datasets

[Leandro Hermida]

Hi again,

Very sorry to ask again, just gotten no repsonse, but is this a Galaxy bug
or does anyone have a functioning tool that takes multiple datasets as an
input parameter??? i.e.



regards,
Leandro

On Thu, May 19, 2011 at 7:15 PM, Leandro Hermida  wrote:

> Hi again,
>
> I tried changing the format to txt and tabular which I have other datasets
> in my history and still the same error and stack trace in Galaxy.
>
> Is it possible at all to have a select multiple of datasets as an input
> parameter??
>
> best,
> Leandro
>
>
> On Thu, May 19, 2011 at 6:59 PM, Leandro Hermida <
> soft...@leandrohermida.com> wrote:
>
>> Hi Galaxy developers,
>>
>> Something seems maybe to be wrong with the format="html" type... I forgot
>> to add before that my tool input param the format="html" attribute:
>>
>> 
>>
>> In another tool I have it outputs format="html" and this works and
>> displays in Galaxy just fine. I would like to use multiple of these output
>> datasets in my history as the input for this other tool but something seems
>> to be wrong if you try to do this?
>>
>> a bit lost,
>> Leandro
>>
>>
>> On Thu, May 19, 2011 at 3:30 PM, Leandro Hermida <
>> soft...@leandrohermida.com> wrote:
>>
>>> Hi,
>>>
>>> I have a tool where the input is multi-select of datasets, e.g.:
>>>
>>> 
>>>
>>> I tested it to see what it would pass to my command and I get the
>>> following debug page and error in Galaxy:
>>>
>>> AttributeError: 'list' object has no attribute 'missing_meta'
>>>
>>> The last part of the stack trace looks like:
>>>
>>> >>  validator.validate( value, history )
>>> Module galaxy.tools.parameters.validation:185 in validate
>>>
>>> history 
>>> self>> at 0xb8e6250>
>>> value [,
>>> ]
>>>
>>> >>  if value and value.missing_meta( check = self.check, skip = self.skip
>>> ):
>>> AttributeError: 'list' object has no attribute 'missing_meta'
>>>
>>> What am I doing wrong?
>>>
>>> regards,
>>> Leandro
>>>
>>>
>>
>
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Re: [galaxy-dev] Checkboxes/booleans in tools, again

[Leandro Hermida]

Not everything works correctly with checkbox booleans, the bug a couple
people and I reported long ago

https://bitbucket.org/galaxy/galaxy-central/issue/393/cant-use-checkbox-boolean-with-conditional

is still there.

2011/5/23 Peter Cock 

> 2011/5/23 Louise-Amélie Schmitt :
> > Hello,
> >
> > I know this is still not fully implemented and that there has already
> been a
> > lot of messages on the topic, but I just would like to know if there's a
> way
> > to make the "checked" attribute in the param tags have the required
> effect.
>
> It might help if you were more precise - what isn't working for you?
>
> Ideally there would be an issue already reported on this on bitbucket.
> https://bitbucket.org/galaxy/galaxy-central/issues?sort=-id
>
> As I recall, the checked attribute is working fine for boolean parameters:
> https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
>
> Peter
>
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Re: [galaxy-dev] select multiple tool input parameter bugs?

[Leandro Hermida]

Hi again,

I think I've figured out the bug... it seems that you cannot do
selected="true" on any options with a select multiple input param.  If you
remove those then everything displays properly, but unfortunately you cannot
configure a set of default selected options for when the form comes up.

best,
Leandro

On Thu, May 19, 2011 at 7:12 PM, Leandro Hermida  wrote:

> I have the following tool input parameter:
>
> 
> SIZE
> ES
> NES
> NOM p-val
> FDR q-val
> FWER p-val
> RANK AT MAX
> LEADING EDGE
> 
>
> It displays a single select drop-down menu, is this a bug or did I
> configure something wrong?
>
> To check I added display="checkboxes" to the param above and now it
> displays a multi select but when the form loads everything comes up checked
> it doesn't obey any of the selected="true"? Is this also a bug or must it be
> done a different way?
>
> regards,
> Leandro
>
>
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Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple="true" input datasets

[Leandro Hermida]

Hi again,

I tried changing the format to txt and tabular which I have other datasets
in my history and still the same error and stack trace in Galaxy.

Is it possible at all to have a select multiple of datasets as an input
parameter??

best,
Leandro

On Thu, May 19, 2011 at 6:59 PM, Leandro Hermida  wrote:

> Hi Galaxy developers,
>
> Something seems maybe to be wrong with the format="html" type... I forgot
> to add before that my tool input param the format="html" attribute:
>
> 
>
> In another tool I have it outputs format="html" and this works and displays
> in Galaxy just fine. I would like to use multiple of these output datasets
> in my history as the input for this other tool but something seems to be
> wrong if you try to do this?
>
> a bit lost,
> Leandro
>
>
> On Thu, May 19, 2011 at 3:30 PM, Leandro Hermida <
> soft...@leandrohermida.com> wrote:
>
>> Hi,
>>
>> I have a tool where the input is multi-select of datasets, e.g.:
>>
>> 
>>
>> I tested it to see what it would pass to my command and I get the
>> following debug page and error in Galaxy:
>>
>> AttributeError: 'list' object has no attribute 'missing_meta'
>>
>> The last part of the stack trace looks like:
>>
>> >>  validator.validate( value, history )
>> Module galaxy.tools.parameters.validation:185 in validate
>>
>> history 
>> self> at 0xb8e6250>
>> value [,
>> ]
>>
>> >>  if value and value.missing_meta( check = self.check, skip = self.skip
>> ):
>> AttributeError: 'list' object has no attribute 'missing_meta'
>>
>> What am I doing wrong?
>>
>> regards,
>> Leandro
>>
>>
>
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[galaxy-dev] select multiple tool input parameter bugs?

[Leandro Hermida]

I have the following tool input parameter:


SIZE
ES
NES
NOM p-val
FDR q-val
FWER p-val
RANK AT MAX
LEADING EDGE


It displays a single select drop-down menu, is this a bug or did I configure
something wrong?

To check I added display="checkboxes" to the param above and now it displays
a multi select but when the form loads everything comes up checked it
doesn't obey any of the selected="true"? Is this also a bug or must it be
done a different way?

regards,
Leandro
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Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple="true" input datasets

[Leandro Hermida]

Hi Galaxy developers,

Something seems maybe to be wrong with the format="html" type... I forgot to
add before that my tool input param the format="html" attribute:



In another tool I have it outputs format="html" and this works and displays
in Galaxy just fine. I would like to use multiple of these output datasets
in my history as the input for this other tool but something seems to be
wrong if you try to do this?

a bit lost,
Leandro

On Thu, May 19, 2011 at 3:30 PM, Leandro Hermida  wrote:

> Hi,
>
> I have a tool where the input is multi-select of datasets, e.g.:
>
> 
>
> I tested it to see what it would pass to my command and I get the following
> debug page and error in Galaxy:
>
> AttributeError: 'list' object has no attribute 'missing_meta'
>
> The last part of the stack trace looks like:
>
> >>  validator.validate( value, history )
> Module galaxy.tools.parameters.validation:185 in validate
>
> history 
> self 0xb8e6250>
> value [,
> ]
>
> >>  if value and value.missing_meta( check = self.check, skip = self.skip
> ):
> AttributeError: 'list' object has no attribute 'missing_meta'
>
> What am I doing wrong?
>
> regards,
> Leandro
>
>
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Re: [galaxy-dev] Specifying number of requested cores to Galaxy DRMAA

[Leandro Hermida]

Hi Louise,

I see thank you for the response, maybe there was some confusion, the
feature I was trying to explain with LSF is that you *don't* need to tell it
the required resources for a job and it will still be able to run all the
submitted jobs on a node without crashing even if the jobs submitted need
e.g. 10 more cores are available (that is 10 more cores than LSF thought it
needed).  LSF will just temporarily suspend jobs in mid-run on a node to
keep the load down, but nothing will ever crash even if you are running jobs
that require 20 CPUs and you only have 2.  Thought maybe there was a way to
do this with TORQUE.  If LSF or TORQUE are explcitly passed the resources
needed then they will never need to temporarily suspend because they will
pick a node with those resources free.  That being said, your method is more
efficient for this reason as it will pick the right node with the cores
available instead of picking a node with maybe just one core available and
then running the multithreaded job slower because it has to periodically
suspend it as it is running.

Also I wonder do you run any Java command-line tools via Galaxy? I can't
seem to find with the JVM exactly how many cores it needs during execution
or how to limit it to a certain max, it just jumps around in CPU usage from
50% to over 400%

regards,
Leandro

2011/5/19 Louise-Amélie Schmitt 

>  Hi again Leandro
>
> Well I might not have been really clear, perhaps I should have re-read the
> mail before posting it :)
>
> The thing is, it was not an issue of Torque starting jobs when there were
> not enough resources available, but rather it believing the needed resources
> for each job being fewer that they were (e.g. always assuming the jobs were
> single-threaded even if the actual tools needed more tan one core). if
> Torque is properly notified of the needed resources, it will dispatch them
> or make them wait accordingly (since it knows the nodes' limits and load),
> like your LSF does.
>
> This hack is not very sexy but it just notifies Torque of the cores needed
> by every multithreaded tool, so it doesn't run a multithreaded job when
> there's only one core available in the chosen node.
>
> Hope that helps :)
>
> Regards,
> L-A
>
>
>
> On 05/19/2011 03:05 PM, Leandro Hermida wrote:
>
> Hi Louise-Amelie,
>
> Thank you for the post reference, this is exactly what I was looking for.
> For us for for example when I want to execute a tool that is a Java command
> the JVM typically will typically use multiple cores as it's running.  You
> said with TORQUE it will crash when there aren't enough resources when the
> job is submitted.  I wonder if you can do the same thing we have done here
> with LSF?  With LSF you can configure a maximum server load for each node
> and if the submitted jobs push the node load above this threshold (e.g. more
> cores requested than available) LSF will temporarily suspend jobs (using
> some kind of heuristics) so that the load stays below the threshold and
> unsuspend as resources become available.  So for us things just will run
> slower when we cannot pass the requested number of cores to LSF.
>
> I would think maybe there is a way with TORQUE to have it achieve the same
> thing so jobs don't crash when resources requested are more than available?
>
> regards,
> Leandro
>
> 2011/5/19 Louise-Amélie Schmitt 
>
>>  Hi,
>>
>> In a previous message, I explained how I did to multithreads certain jobs,
>> perhaps you can modify the corresponding files for drmaa in a similar way:
>>
>> On 04/26/2011 11:26 AM, Louise-Amélie Schmitt wrote:
>>
>> Just one little fix on line 261:
>> 261 if ( len(l) > 1 and l[0] == job_wrapper.tool.id ):
>>
>> Otherwise it pathetically crashes when non-multithreaded jobs are
>> submitted. Sorry about that.
>>
>> Regards,
>> L-A
>>
>> Le mardi 19 avril 2011 à 14:33 +0200, Louise-Amélie Schmitt a écrit :
>>
>>  Hello everyone,
>>
>> I'm using TORQUE with Galaxy, and we noticed that if a tool is
>> multithreaded, the number of needed cores is not communicated to pbs,
>> leading to job crashes if the required resources are not available when
>> the job is submitted.
>>
>> Therefore I modified a little the code as follows in
>> lib/galaxy/jobs/runners/pbs.py
>>
>> 256 # define PBS job options
>> 257 attrs.append( dict( name = pbs.ATTR_N, value = str( "%s_%s_%
>> s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) ) ) )
>> 258 mt_file = open('tool-data/multithreading.csv', 'r')
>> 259 for l in mt_file:
>> 26

[galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple="true" input datasets

[Leandro Hermida]

Hi,

I have a tool where the input is multi-select of datasets, e.g.:



I tested it to see what it would pass to my command and I get the following
debug page and error in Galaxy:

AttributeError: 'list' object has no attribute 'missing_meta'

The last part of the stack trace looks like:

>>  validator.validate( value, history )
Module galaxy.tools.parameters.validation:185 in validate

history 
self
value [,
]

>>  if value and value.missing_meta( check = self.check, skip = self.skip ):
AttributeError: 'list' object has no attribute 'missing_meta'

What am I doing wrong?

regards,
Leandro
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Re: [galaxy-dev] wait thread: <1002:Not enough memory.> error > after enabling DRMAA

[Leandro Hermida]

Hi Mariusz,

In another Galaxy post Marina had mentioned it is a bug with the latest
FedStage LSF DRMAA 1.0.4 implementation.

If you build and use the previous 1.0.3 version it works fine and you don't
get this error.

regards,
Leandro

2011/5/19 Mariusz Mamoński 

> Hi,
>
> > --
> >
> > Message: 13
> > Date: Wed, 18 May 2011 17:15:06 +0200
> > From: Leandro Hermida 
> > To: Galaxy Dev 
> > Subject: [galaxy-dev] wait thread: <1002:Not enough memory.> error
> >after   enabling DRMAA
> > Message-ID: 
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hi all,
> >
> > I enabled DRMAA on my test Galaxy server installation and in the server
> > startup output I get the following  strange "E #14ca [ 1.10]  * wait
>
>
> are you using LSF?
>
>
> > thread: <1002:Not enough memory.>" lines after loading the job manager:
> >
> > ...
> > galaxy.jobs.runners.local INFO 2011-05-18 17:10:23,025 starting workers
> > galaxy.jobs.runners.local DEBUG 2011-05-18 17:10:23,026 5 workers ready
> > galaxy.jobs DEBUG 2011-05-18 17:10:23,026 Loaded job runner:
> > galaxy.jobs.runners.local:LocalJobRunner
> > galaxy.jobs.runners.drmaa DEBUG 2011-05-18 17:10:23,130 3 workers ready
> > galaxy.jobs DEBUG 2011-05-18 17:10:23,130 Loaded job runner:
> > galaxy.jobs.runners.drmaa:DRMAAJobRunner
> > galaxy.jobs INFO 2011-05-18 17:10:23,131 job manager started
> > E #14ca [ 0.00]  * wait thread: <1002:Not enough memory.>
> > E #14ca [ 0.02]  * wait thread: <1002:Not enough memory.>
> > E #14ca [ 0.05]  * wait thread: <1002:Not enough memory.>
> > E #14ca [ 0.07]  * wait thread: <1002:Not enough memory.>
> > E #14ca [ 0.10]  * wait thread: <1002:Not enough memory.>
> > E #14ca [ 0.12]  * wait thread: <1002:Not enough memory.>
> > E #14ca [ 0.15]  * wait thread: <1002:Not enough memory.>
> > E #14ca [ 0.17]  * wait thread: <1002:Not enough memory.>
> > E #14ca [ 0.20]  * wait thread: <1002:Not enough memory.>
> > galaxy.jobs INFO 2011-05-18 17:10:23,373 job stopper started
> > E #14ca [ 0.22]  * wait thread: <1002:Not enough memory.>
> > galaxy.sample_tracking.external_service_types DEBUG 2011-05-18
> 17:10:23,383
> > Loaded external_service_type: Simple unknown sequencer 1.0.0
> > galaxy.sample_tracking.external_service_types DEBUG 2011-05-18
> 17:10:23,386
> > Loaded external_service_type: Applied Biosystems SOLiD 1.0.0
> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,400 Enabling 'admin'
> > controller, class: AdminGalaxy
> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,402 Enabling 'async'
> > controller, class: ASync
> > E #14ca [ 0.25]  * wait thread: <1002:Not enough memory.>
> > E #14ca [ 0.27]  * wait thread: <1002:Not enough memory.>
> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,428 Enabling
> 'dataset'
> > controller, class: DatasetInterface
> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,432 Enabling 'error'
> > controller, class: Error
> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,436 Enabling
> > 'external_service' controller, class: ExternalService
> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,437 Enabling
> > 'external_services' controller, class: ExternalServiceController
> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,439 Enabling 'forms'
> > controller, class: Forms
> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,441 Enabling
> 'history'
> > controller, class: HistoryController
> > E #14ca [ 0.30]  * wait thread: <1002:Not enough memory.>
> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,460 Enabling
> 'library'
> > controller, class: Library
> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,461 Enabling
> > 'library_admin' controller, class: LibraryAdmin
> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,462 Enabling
> > 'library_common' controller, class: LibraryCommon
> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,475 Enabling 'mobile'
> > controller, class: Mobile
> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,478 Enabling 'page'
> > controller, class: PageController
> > E #14ca [ 0.32]  * wait thread: <1002:Not enough memory.>
> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,482 Enabling
> > '

Re: [galaxy-dev] Specifying number of requested cores to Galaxy DRMAA

[Leandro Hermida]

Hi Louise-Amelie,

Thank you for the post reference, this is exactly what I was looking for.
For us for for example when I want to execute a tool that is a Java command
the JVM typically will typically use multiple cores as it's running.  You
said with TORQUE it will crash when there aren't enough resources when the
job is submitted.  I wonder if you can do the same thing we have done here
with LSF?  With LSF you can configure a maximum server load for each node
and if the submitted jobs push the node load above this threshold (e.g. more
cores requested than available) LSF will temporarily suspend jobs (using
some kind of heuristics) so that the load stays below the threshold and
unsuspend as resources become available.  So for us things just will run
slower when we cannot pass the requested number of cores to LSF.

I would think maybe there is a way with TORQUE to have it achieve the same
thing so jobs don't crash when resources requested are more than available?

regards,
Leandro

2011/5/19 Louise-Amélie Schmitt 

>  Hi,
>
> In a previous message, I explained how I did to multithreads certain jobs,
> perhaps you can modify the corresponding files for drmaa in a similar way:
>
> On 04/26/2011 11:26 AM, Louise-Amélie Schmitt wrote:
>
> Just one little fix on line 261:
> 261 if ( len(l) > 1 and l[0] == job_wrapper.tool.id ):
>
> Otherwise it pathetically crashes when non-multithreaded jobs are
> submitted. Sorry about that.
>
> Regards,
> L-A
>
> Le mardi 19 avril 2011 à 14:33 +0200, Louise-Amélie Schmitt a écrit :
>
>  Hello everyone,
>
> I'm using TORQUE with Galaxy, and we noticed that if a tool is
> multithreaded, the number of needed cores is not communicated to pbs,
> leading to job crashes if the required resources are not available when
> the job is submitted.
>
> Therefore I modified a little the code as follows in
> lib/galaxy/jobs/runners/pbs.py
>
> 256 # define PBS job options
> 257 attrs.append( dict( name = pbs.ATTR_N, value = str( "%s_%s_%
> s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) ) ) )
> 258 mt_file = open('tool-data/multithreading.csv', 'r')
> 259 for l in mt_file:
> 260 l = string.split(l)
> 261 if ( l[0] == job_wrapper.tool.id ):
> 262 attrs.append( dict( name = pbs.ATTR_l,
> resource = 'nodes', value = '1:ppn='+str(l[1]) ) )
> 263 attrs.append( dict( name = pbs.ATTR_l,
> resource = 'mem', value = str(l[2]) ) )
> 264 break
> 265 mt_file.close()
> 266 job_attrs = pbs.new_attropl( len( attrs ) +
> len( pbs_options ) )
>
> (sorry it didn't come out very well due to line breaking)
>
> The csv file contains a list of the multithreaded tools, each line
> containing:
> \t\t\n
>
> And it works fine, the jobs wait for their turn properly, but
> information is duplicated. Perhaps there would be a way to include
> something similar in galaxy's original code (if it is not already the
> case, I may not be up-to-date) without duplicating data.
>
> I hope that helps :)
>
> Best regards,
> L-A
>
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>
>
> On 05/19/2011 12:03 PM, Leandro Hermida wrote:
>
> Hi,
>
> When Galaxy is configured to use the DRMAA job runner is there a way for a
> tool to tell DRMAA the number of cores it would like to request? The
> equivalent of bsub -n X in LSF where X is min number of cores to have
> available on node.
>
> best,
> leandro
>
>
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Re: [galaxy-dev] issue with LSB_DEFAULTQUEUE

[Leandro Hermida]

Thanks Marina this works perfectly, everything fully operational now very
glad for your help!

-Leandro

On Thu, May 19, 2011 at 2:23 PM, Marina Gourtovaia  wrote:

>  Hi Leandro
>
> I do not think the binding is env var aware. I used the following string in
> Galaxy drmaa configuration in universe_wsgi.ini
>
> default_cluster_job_runner = drmaa://-q srpipeline -P pipeline/
>
> -q for the queue and -P for the project
>
> Marina
>
>
>
> On 19/05/2011 12:54, Leandro Hermida wrote:
>
> Hi Marina,
>
> Thank you so much for your help, LSF DRMAA is working fine with Galaxy now.
>
> One final problem though... if I specify the env var LSB_DEFAULTQUEUE to a
> specific queue the Galaxy server appears in the log to submit the job but it
> doesn't ever seem to get executed and looking in LSF with bjobs -u all we
> don't see any galaxy submitted jobs, strange.  Is there something I am not
> setting up right with the particular queue?
>
> best,
> Leandro
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a company
> registered in England with number 2742969, whose registered office is 215
> Euston Road, London, NW1 2BE.
>
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[galaxy-dev] nice quality Galaxy logo and name

[Leandro Hermida]

Hi there,

Would anyone have a nice quality Galaxy logo and name image for
presentations and posters?  I've been using the one in the left hand corner
of the server which ok but wondering if there is a better official one or
something

regards,
leandro
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[galaxy-dev] Specifying number of requested cores to Galaxy DRMAA

[Leandro Hermida]

Hi,

When Galaxy is configured to use the DRMAA job runner is there a way for a
tool to tell DRMAA the number of cores it would like to request? The
equivalent of bsub -n X in LSF where X is min number of cores to have
available on node.

best,
leandro
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Re: [galaxy-dev] wait thread: <1002:Not enough memory.> error after enabling DRMAA

[Leandro Hermida]

Hi Marina,

Thanks... so are you using 1.0.3 instead of 1.0.4?

best,
leandro

On Wed, May 18, 2011 at 6:56 PM, Marina Gourtovaia  wrote:

>  Hi Leandro
>
> From our previous correspondence I remember that you are using LSF
> This is some sort of a bug in the latest drmaa-lsf binding. I moved to the
> previous version and everything is OK for me
>
> Marina
>
>
> On 18/05/2011 16:15, Leandro Hermida wrote:
>
> Hi all,
>
> I enabled DRMAA on my test Galaxy server installation and in the server
> startup output I get the following  strange "E #14ca [ 1.10]  * wait
> thread: <1002:Not enough memory.>" lines after loading the job manager:
>
> ...
> galaxy.jobs.runners.local INFO 2011-05-18 17:10:23,025 starting workers
> galaxy.jobs.runners.local DEBUG 2011-05-18 17:10:23,026 5 workers ready
> galaxy.jobs DEBUG 2011-05-18 17:10:23,026 Loaded job runner:
> galaxy.jobs.runners.local:LocalJobRunner
> galaxy.jobs.runners.drmaa DEBUG 2011-05-18 17:10:23,130 3 workers ready
> galaxy.jobs DEBUG 2011-05-18 17:10:23,130 Loaded job runner:
> galaxy.jobs.runners.drmaa:DRMAAJobRunner
> galaxy.jobs INFO 2011-05-18 17:10:23,131 job manager started
> E #14ca [ 0.00]  * wait thread: <1002:Not enough memory.>
> E #14ca [ 0.02]  * wait thread: <1002:Not enough memory.>
> E #14ca [ 0.05]  * wait thread: <1002:Not enough memory.>
> E #14ca [ 0.07]  * wait thread: <1002:Not enough memory.>
> E #14ca [ 0.10]  * wait thread: <1002:Not enough memory.>
> E #14ca [ 0.12]  * wait thread: <1002:Not enough memory.>
> E #14ca [ 0.15]  * wait thread: <1002:Not enough memory.>
> E #14ca [ 0.17]  * wait thread: <1002:Not enough memory.>
> E #14ca [ 0.20]  * wait thread: <1002:Not enough memory.>
> galaxy.jobs INFO 2011-05-18 17:10:23,373 job stopper started
> E #14ca [ 0.22]  * wait thread: <1002:Not enough memory.>
> galaxy.sample_tracking.external_service_types DEBUG 2011-05-18 17:10:23,383
> Loaded external_service_type: Simple unknown sequencer 1.0.0
> galaxy.sample_tracking.external_service_types DEBUG 2011-05-18 17:10:23,386
> Loaded external_service_type: Applied Biosystems SOLiD 1.0.0
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,400 Enabling 'admin'
> controller, class: AdminGalaxy
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,402 Enabling 'async'
> controller, class: ASync
> E #14ca [ 0.25]  * wait thread: <1002:Not enough memory.>
> E #14ca [ 0.27]  * wait thread: <1002:Not enough memory.>
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,428 Enabling 'dataset'
> controller, class: DatasetInterface
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,432 Enabling 'error'
> controller, class: Error
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,436 Enabling
> 'external_service' controller, class: ExternalService
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,437 Enabling
> 'external_services' controller, class: ExternalServiceController
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,439 Enabling 'forms'
> controller, class: Forms
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,441 Enabling 'history'
> controller, class: HistoryController
> E #14ca [ 0.30]  * wait thread: <1002:Not enough memory.>
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,460 Enabling 'library'
> controller, class: Library
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,461 Enabling
> 'library_admin' controller, class: LibraryAdmin
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,462 Enabling
> 'library_common' controller, class: LibraryCommon
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,475 Enabling 'mobile'
> controller, class: Mobile
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,478 Enabling 'page'
> controller, class: PageController
> E #14ca [ 0.32]  * wait thread: <1002:Not enough memory.>
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,482 Enabling
> 'request_type' controller, class: RequestType
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,483 Enabling 'requests'
> controller, class: Requests
> E #14ca [ 0.35]  * wait thread: <1002:Not enough memory.>
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,508 Enabling
> 'requests_admin' controller, class: RequestsAdmin
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,509 Enabling
> 'requests_common' controller, class: RequestsCommon
> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,511 Enabling 'root'
> controller, c

[galaxy-dev] Increase select multiple menu width for tag type="data"

[Leandro Hermida]

Hi,

Is there a way to increase the width of a select multiple menu for a 
tag type="data"?  Certain dataset labels I have are very informative :)
(i.e. long) and when used as an input to a tool you can't read what the
difference is between each item unless you look at the dataset number and
look back at the history.

regards,
Leandro
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[galaxy-dev] wait thread: <1002:Not enough memory.> error after enabling DRMAA

[Leandro Hermida]

Hi all,

I enabled DRMAA on my test Galaxy server installation and in the server
startup output I get the following  strange "E #14ca [ 1.10]  * wait
thread: <1002:Not enough memory.>" lines after loading the job manager:

...
galaxy.jobs.runners.local INFO 2011-05-18 17:10:23,025 starting workers
galaxy.jobs.runners.local DEBUG 2011-05-18 17:10:23,026 5 workers ready
galaxy.jobs DEBUG 2011-05-18 17:10:23,026 Loaded job runner:
galaxy.jobs.runners.local:LocalJobRunner
galaxy.jobs.runners.drmaa DEBUG 2011-05-18 17:10:23,130 3 workers ready
galaxy.jobs DEBUG 2011-05-18 17:10:23,130 Loaded job runner:
galaxy.jobs.runners.drmaa:DRMAAJobRunner
galaxy.jobs INFO 2011-05-18 17:10:23,131 job manager started
E #14ca [ 0.00]  * wait thread: <1002:Not enough memory.>
E #14ca [ 0.02]  * wait thread: <1002:Not enough memory.>
E #14ca [ 0.05]  * wait thread: <1002:Not enough memory.>
E #14ca [ 0.07]  * wait thread: <1002:Not enough memory.>
E #14ca [ 0.10]  * wait thread: <1002:Not enough memory.>
E #14ca [ 0.12]  * wait thread: <1002:Not enough memory.>
E #14ca [ 0.15]  * wait thread: <1002:Not enough memory.>
E #14ca [ 0.17]  * wait thread: <1002:Not enough memory.>
E #14ca [ 0.20]  * wait thread: <1002:Not enough memory.>
galaxy.jobs INFO 2011-05-18 17:10:23,373 job stopper started
E #14ca [ 0.22]  * wait thread: <1002:Not enough memory.>
galaxy.sample_tracking.external_service_types DEBUG 2011-05-18 17:10:23,383
Loaded external_service_type: Simple unknown sequencer 1.0.0
galaxy.sample_tracking.external_service_types DEBUG 2011-05-18 17:10:23,386
Loaded external_service_type: Applied Biosystems SOLiD 1.0.0
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,400 Enabling 'admin'
controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,402 Enabling 'async'
controller, class: ASync
E #14ca [ 0.25]  * wait thread: <1002:Not enough memory.>
E #14ca [ 0.27]  * wait thread: <1002:Not enough memory.>
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,428 Enabling 'dataset'
controller, class: DatasetInterface
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,432 Enabling 'error'
controller, class: Error
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,436 Enabling
'external_service' controller, class: ExternalService
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,437 Enabling
'external_services' controller, class: ExternalServiceController
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,439 Enabling 'forms'
controller, class: Forms
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,441 Enabling 'history'
controller, class: HistoryController
E #14ca [ 0.30]  * wait thread: <1002:Not enough memory.>
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,460 Enabling 'library'
controller, class: Library
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,461 Enabling
'library_admin' controller, class: LibraryAdmin
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,462 Enabling
'library_common' controller, class: LibraryCommon
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,475 Enabling 'mobile'
controller, class: Mobile
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,478 Enabling 'page'
controller, class: PageController
E #14ca [ 0.32]  * wait thread: <1002:Not enough memory.>
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,482 Enabling
'request_type' controller, class: RequestType
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,483 Enabling 'requests'
controller, class: Requests
E #14ca [ 0.35]  * wait thread: <1002:Not enough memory.>
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,508 Enabling
'requests_admin' controller, class: RequestsAdmin
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,509 Enabling
'requests_common' controller, class: RequestsCommon
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,511 Enabling 'root'
controller, class: RootController
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,514 Enabling 'tag'
controller, class: TagsController
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,519 Enabling
'tool_runner' controller, class: ToolRunner
E #14ca [ 0.37]  * wait thread: <1002:Not enough memory.>
E #14ca [ 0.40]  * wait thread: <1002:Not enough memory.>
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,558 Enabling 'tracks'
controller, class: TracksController
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,562 Enabling
'ucsc_proxy' controller, class: UCSCProxy
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,564 Enabling 'user'
controller, class: User
galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,567 Enabling
'visualization' controller, class: VisualizationController
E #14ca [ 0.42]  * wait thread: <1002:Not enough memory.>
E #14ca [ 0.45]  * wait thread: <1002:Not enough memory.>
E #14ca [ 0.47]  * wait thread: <1002:Not enough memory.>
E #14ca [ 0.50]  * wait thread: <1002:Not enough memory.>
E #14ca [ 0.53]  * wait thread: <100

[galaxy-dev] select menu in conditional tag cannot be set at runtime in workflow editor

[Leandro Hermida]

Hi all,

In a tool XML I have a select menu param within/driving a conditional tag
and in the workflow editor it doesn't let me choose to allow the user to set
this select menu at runtime?  Is this a bug?

best,
leandro
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[galaxy-dev] param type="float" optional="true" doesn't work

[Leandro Hermida]

Hi, how do you make float parameter types fully optional? optional="true"
doesn't work.

-Leandro
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Re: [galaxy-dev] Getting tool dirpath in a Python code file

[Leandro Hermida]

Hi Assaf,

On Thu, Apr 28, 2011 at 7:55 PM, Assaf Gordon  wrote:

> Leandro Hermida wrote, On 04/28/2011 08:55 AM:
> > Hi galaxy developers,
> >
> > Just want to double-check, there is no way to import some kind of galaxy
> tool context info into python code you are running for a tool?
>
> Nothing is impossible... just depends on how messy you want to get :)
>
> for me, the following works:
> ===  python_path.xml  ===
> 
> echo '$input1' > '$output'
>
>
>
>
>
>
>
> 
> ==
>
>  python_path_code.py =
> from os import path
> import sys
>
> def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout,
> stderr):
>tool_path = path.abspath(tool.tool_dir);
>sys.stderr.write("! path = %s\n" % (tool_path))
> 
>
> When the tool runs, the following line is printed to STDERR:
> ==
> ! path = /home/gordon/projects/galaxy_dev/tools/cshl_tests
> ==
>
> Help this helps,
>  -gordon
>

Thanks so much, I never knew of the page
https://bitbucket.org/galaxy/galaxy-central/wiki/CustomCode until seeing
what you wrote and searching now.  But I have one complication I guess.  My
tool is already running a Python code file to dynamically create a drop-down
menu using the dynamic_options attribute a la:


...


In this function my_options I would need the tool dir path.  How would I be
able to combine what you did with this?  Which function runs at the right
time before my_options() is executed is it exec_before_process?


> >
> > best,
> > leandro
> >
> > On Fri, Apr 15, 2011 at 8:03 PM, Leandro Hermida <
> soft...@leandrohermida.com <mailto:soft...@leandrohermida.com>> wrote:
> >
> > On Fri, Apr 15, 2011 at 7:27 PM, Peter Cock <
> p.j.a.c...@googlemail.com <mailto:p.j.a.c...@googlemail.com>> wrote:
> >
> > On Thu, Apr 14, 2011 at 2:56 PM, Leandro Hermida
> > mailto:soft...@leandrohermida.com>>
> wrote:
> > > On Thu, Apr 14, 2011 at 3:17 PM, Peter Cock <
> p.j.a.c...@googlemail.com <mailto:p.j.a.c...@googlemail.com>>
> > > wrote:
> > >>
> > >> For standard Python tools in Galaxy, I'm using
> > >> os.path.split(sys.argv[0])[0]
> > >> to get the path, which on reflection probably should be
> written as
> > >> os.path.dirname(sys.argv[0]) as you suggest.
> > >>
> > >> What do __file__ and sys.argv[0] give you? The simplest way to
> debug
> > >> this is to add a print statement, since Galaxy will show the
> stdout.
> > >>
> > >
> > > Hi Peter,
> > >
> > > __file__ throws an error: global name '__file__' is not defined
> >
> > I guess the script is being loaded as a string, and run with
> eval(...)
> > or something like that. It would also explain why sys.argv[0]
> would
> > be one of the Galaxy script files.
> >
> > > os.path.abspath(os.path.dirname(sys.argv[0])) gives me
> > > /path/to/galaxy/scripts directory which is two levels up from
> what the tool
> > > directory I want for example /path/to/galaxy/tools/mytool
> >
> > So combine that with ../tools/mytool/ and you're done? OK, you
> have
> > to know the name of the folder your tool *should* be in... so not
> a
> > perfect solution.
> >
> >
> > Thanks Peter, yes that's the same idea I did as a quick fix also
> don't like the fact that my tool directory is hard-coded but oh well.  There
> must be a way within Python in Galaxy importing something from Galaxy that
> has the current tool directory path, it would seem that Galaxy needs to know
> this and would store it anyway?
> >
> > best,
> > Leandro
> >
> >
>
>
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Re: [galaxy-dev] anyone actually properly implemented remote_user_logout_href with external HTTP authentication?

[Leandro Hermida]

On Thu, Apr 28, 2011 at 5:52 PM, Nate Coraor  wrote:

> Leandro Hermida wrote:
> > Hi everyone,
> >
> > Has anyone actually properly implemented remote_user_logout_href in
> Galaxy
> > with external HTTP authentication?  As probably those who have tried
> know,
> > it is rife there doesn't seem to be a clean and robust way to do this?
>

It's not a Galaxy-specific issue, it's that it looks impossible to provide
server-side link of some kind (which runs some script, etc.) that executes
some mechanism that will clear the HTTP active login on the browser.  It's
impossible to do that cleanly and robustly unless someone know how to do it?


> Hi Leandro,
>
> Other than loading in the center panel in Galaxy (which I can commit an
> easy fix for), are there other problems with it?
>
> --nate
>
> >
> > best,
> > Leandro
>
> > ___
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> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >
> >   http://lists.bx.psu.edu/
>
>
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Re: [galaxy-dev] User Name "not set" with external LDAP authentication

[Leandro Hermida]

On Thu, Apr 28, 2011 at 5:33 PM, Nate Coraor  wrote:

> Pieter Neerincx wrote:
> > Hi Leandro,
> >
> > On Apr 27, 2011, at 6:08 PM, Leandro Hermida wrote:
> >
> > > Hi Pieter,
> >
> > 
> >
> > > I have this *exact* same setup as you where I am authenticating with
> the LDAP user ID and returning a mail LDAP attribute as REMOTE_USER, but
> this sets the Galaxy user email address (which in Galaxy is the user ID) but
> is *doesn't* set any *User Name*, all my external users have User Name "not
> set".  Are you sure your setup above sets the User Name to something? Check
> under Admin -> Manage Users, under the User Name column all my users that
> are external yes say "not set".
> >
> > Sorry for the confusion. Indeed it's the user ID alias e-mail address
> that is set correctly. The user name is "not set" and I don't know how to
> set it or if that is even possible with the current Galaxy Maybe some of
> the developers can enlighten us...
>
> Correct, this feature was missing.  As of changeset 5469:7c101a11d261
> Galaxy will now set the username to the value preceeding the '@' in the
> email address, or append '-' if that username is taken.  Users
> can modify their username from the 'User' menu in the masthead.
>
> --nate


Thanks Nate for the info.  I would like to add though that this might not
work for many organizations.  Many places have for example:

lhermida as username
leandro.herm...@domain.org as the email address


>
> >
> > Cheers,
> >
> > Pi
> >
> > >  regards,
> > >  Leandro
> >
> > -
> > mobile: +31 6 143 66 783
> > e-mail: pieter.neeri...@gmail.com
> > skype:  pieter.online
> > -
> >
> >
> > ___
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> > and other Galaxy lists, please use the interface at:
> >
> >   http://lists.bx.psu.edu/
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[galaxy-dev] tool parameter attribute for option display value (not passed value)?

[Leandro Hermida]

Hi,

For a tool select input parameter:


Homo sapiens
Mus musculus
Rattus norvegicus


Is there an attribute for the variable $input1 that will give me the
displayed value (e.g. Homo sapiens, not hs33)?

thank you,
Leandro
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Re: [galaxy-dev] Getting tool dirpath in a Python code file

[Leandro Hermida]

Hi galaxy developers,

Just want to double-check, there is no way to import some kind of galaxy
tool context info into python code you are running for a tool?

best,
leandro

On Fri, Apr 15, 2011 at 8:03 PM, Leandro Hermida  wrote:

> On Fri, Apr 15, 2011 at 7:27 PM, Peter Cock wrote:
>
>> On Thu, Apr 14, 2011 at 2:56 PM, Leandro Hermida
>>  wrote:
>> > On Thu, Apr 14, 2011 at 3:17 PM, Peter Cock 
>> > wrote:
>> >>
>> >> For standard Python tools in Galaxy, I'm using
>> >> os.path.split(sys.argv[0])[0]
>> >> to get the path, which on reflection probably should be written as
>> >> os.path.dirname(sys.argv[0]) as you suggest.
>> >>
>> >> What do __file__ and sys.argv[0] give you? The simplest way to debug
>> >> this is to add a print statement, since Galaxy will show the stdout.
>> >>
>> >
>> > Hi Peter,
>> >
>> > __file__ throws an error: global name '__file__' is not defined
>>
>> I guess the script is being loaded as a string, and run with eval(...)
>> or something like that. It would also explain why sys.argv[0] would
>> be one of the Galaxy script files.
>>
>> > os.path.abspath(os.path.dirname(sys.argv[0])) gives me
>> > /path/to/galaxy/scripts directory which is two levels up from what the
>> tool
>> > directory I want for example /path/to/galaxy/tools/mytool
>>
>> So combine that with ../tools/mytool/ and you're done? OK, you have
>> to know the name of the folder your tool *should* be in... so not a
>> perfect solution.
>
>
> Thanks Peter, yes that's the same idea I did as a quick fix also don't
> like the fact that my tool directory is hard-coded but oh well.  There must
> be a way within Python in Galaxy importing something from Galaxy that has
> the current tool directory path, it would seem that Galaxy needs to know
> this and would store it anyway?
>
> best,
> Leandro
>
>
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Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

[Leandro Hermida]

Hi again,

Can one via the API upload a file programmatically just like one does using
the UI?

best,
Leandro

On Wed, Apr 27, 2011 at 3:43 PM, Dannon Baker  wrote:

> Not currently, though the API is being continually extended with new
> features as the need arises.
>
> -Dannon
>
> On Apr 27, 2011, at 9:40 AM, Leandro Hermida wrote:
> > Hi Dannon,
> >
> > Thanks for your replies and advice, this leads me to a quesion... is it
> possible to execute a tool job via the Galaxy API just like someone does via
> the UI? Could I then have a tool script that wraps this programmatic
> execution of X tool jobs via the API?
> >
> > regards,
> > Leandro
>
>
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[galaxy-dev] anyone actually properly implemented remote_user_logout_href with external HTTP authentication?

[Leandro Hermida]

Hi everyone,

Has anyone actually properly implemented remote_user_logout_href in Galaxy
with external HTTP authentication?  As probably those who have tried know,
it is rife there doesn't seem to be a clean and robust way to do this?

best,
Leandro
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Re: [galaxy-dev] User Name "not set" with external LDAP authentication

[Leandro Hermida]

Hi Pieter,

On Wed, Apr 27, 2011 at 4:14 PM, Pieter Neerincx
wrote:

> Hi Leandro,
>
> On Apr 27, 2011, at 3:50 PM, Leandro Hermida wrote:
>
> > Hi,
> >
> > Just wondering if I got my setup right, I have Galaxy front-ended by
> Apache doing the static caching, proxying and LDAP auth.  What's nice is
> that user's don't have to be created by an admin if the user authenticates
> and authorizes properly against the LDAP config then Galaxy will
> automatically create the user locally.
> >
> > My question is that it shows that the User Name is "not set" for such
> users, is this the way its supposed to be
>
> No


> > or can I modify my LDAP config in such a way that it does set a User
> Name?
>
> Yes, you can. I have a similar setup:
>
>#
># For short logins. (Requires rewriting AuthLDAPBindDN to long form.)
>#
>AuthLDAPURL "ldap://
> ldap.uu.nl/ou=medewerkers,o=uu?uuShortID,uuMail"
>AuthLDAPBindDN  "uid=${REMOTE_USER}@soliscom.uu.nl
> ,ou=medewerkers,o=uu"
>#
># Pass the user's e-mail address on to Galaxy as "login"
>#
>RewriteEngine On
>RequestHeader set REMOTE_USER %{AUTHENTICATE_UUMAIL}e
>
> Note that the uuMail attribute requested via the AuthLDAPURL somehow gets
> expanded into an AUTHENTICATE_UUMAIL environment variable, which can then be
> used to rewrite "REMOTE_USER". You should be able to get something similar,
> but the exact syntax will depend on the attributes defined in your LDAP.
> Note that the example above allows my users to login with the part of their
> account before the @. Since the domain part after the @ is the same for all
> of them (soliscom.uu.nl), this saves them some typing when logging in :).
> Their e-mail addresses may be different though, so I rewrite the REMOTE_USER
> to display their e-mail address as Galaxy "account" in the web interface.
>

I have this *exact* same setup as you where I am authenticating with the
LDAP user ID and returning a mail LDAP attribute as REMOTE_USER, but this
sets the Galaxy user email address (which in Galaxy is the user ID) but is
*doesn't* set any *User Name*, all my external users have User Name "not
set".  Are you sure your setup above sets the User Name to something? Check
under Admin -> Manage Users, under the User Name column all my users that
are external yes say "not set".


> Cheers,
>
> Pi
>
> > regards,
> > Leandro
>
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[galaxy-dev] User Name "not set" with external LDAP authentication

[Leandro Hermida]

Hi,

Just wondering if I got my setup right, I have Galaxy front-ended by Apache
doing the static caching, proxying and LDAP auth.  What's nice is that
user's don't have to be created by an admin if the user authenticates and
authorizes properly against the LDAP config then Galaxy will automatically
create the user locally.

My question is that it shows that the User Name is "not set" for such users,
is this the way its supposed to be or can I modify my LDAP config in such a
way that it does set a User Name?

regards,
Leandro
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Re: [galaxy-dev] Does REMOTE_USER have to be an email address?

[Leandro Hermida]

Hi everyone,

To answer my own question after testing various front-end auth setups it
looks like REMOTE_USER must be the email address, and what's nice about LDAP
is that you can have users authenticate with a username or other ID that is
not the email address and still return the email address to Galaxy, if
anyone needs help with such an LDAP configuration please ask me I have it
working with Apache mod_authnz_ldap against Active Directory.

regards,
Leandro

On Fri, Apr 8, 2011 at 7:07 PM, Leandro Hermida
wrote:

> Hello,
>
> When returning REMOTE_USER env var from the external authentication method
> does it have to be an email address for Galaxy? The docs aren't very clear
> on that, in the main External Authentication section it says you have to
> have to set remote_user_maildomain if you aren't return an email address
> (and the domain will be appended it seems) but in the mod_authnz_ldap
> section it says you are allowed to set any attribute to return as
> REMOTE_USER.
>
> regards,
> Leandro
>
>
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Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

[Leandro Hermida]

On Thu, Apr 21, 2011 at 2:40 PM, Dannon Baker  wrote:

> Leandro,
>
> I see what you mean, I misunderstood your original goal.  There currently
> isn't a way to execute single tools in this fashion.
>
> It isn't exactly straightforward, but you could construct a workflow that
> consisted of two steps-- an Input Dataset step, and whatever tool you wanted
> to use, and then you'd be able to use the functionality described in this
> thread as long as your instance is at 5386:67a19816034b or higher.
>
> -Dannon
>

Hi Dannon,

Thanks for your replies and advice, this leads me to a quesion... is it
possible to execute a tool job via the Galaxy API just like someone does via
the UI? Could I then have a tool script that wraps this programmatic
execution of X tool jobs via the API?

regards,
Leandro



>
>
>

>
>
> On Apr 21, 2011, at 7:49 AM, Leandro Hermida wrote:
>
> > Hi again,
> >
> > Sorry to maybe not understand how to get started, but I'm trying for
> something even without the added complexity of a workflow.
> >
> > If you could point me into the right direction: how would I have a single
> tool where on the tool form there is a multi-select of certain datasets in
> the user's history.  The user multi selects X datasets in the form and hits
> submit and Galaxy will launch X tool jobs (on for each of the datasets) at
> the same time in the history.
> >
> > How do I go about doing this?
> >
> > Sorry for being daft,
> > Leandro
> >
> >
> > On Tue, Apr 19, 2011 at 4:34 PM, Dave Walton 
> wrote:
> > Is the server below down?  I'm trying to get there this morning and
> having
> > no luck...
> >
> >
> https://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project#Loop_over_files
> > _in_a_directory
> >
> > Dave
> >
> >
> > On 4/15/11 12:16 PM, "Pieter Neerincx" 
> wrote:
> >
> > > Hi,
> > >
> > > You're not alone with this request! Unfortunately I wasn't able to join
> the
> > > 2-day Galaxy Hackathon, but I heard from a colleague who just came back
> that
> > > this was one of the topics they worked on. At the end of the hackathon
> they
> > > had a working prototype:
> > >
> > >
> https://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project#Loop_over_files_i
> > > n_a_directory
> > >
> > > Since they had only 2 days, it will need some polish, but I heard this
> hack
> > > already made it into the development branch of Galaxy, so we may see
> something
> > > like this in the near future :)
> > >
> > > Cheers,
> > >
> > > Pi
> > >
> > > On Apr 15, 2011, at 4:28 PM, Dave Walton wrote:
> > >
> > >> I've essentially asked the same question of the list in the past and
> gotten
> > >> no real response.
> > >>
> > >> I have the same interest, but from a workflow perspective.
> > >>
> > >> * A module that allows me to select multiple datafiles (say fastq
> files)
> > >> * Then pass each data file to a separate instance of a workflow that
> runs
> > >> tophat and cufflinks
> > >> * then another module that takes the final outputs of each of the
> workflow
> > >> runs and sends them to a final module that merges results.
> > >>
> > >> I am attempting to implement something like this using the API, though
> the
> > >> API is still pretty green from my perspective.
> > >>
> > >> I think functionality like this built into the workflow editor would
> be a
> > >> great addition.
> > >>
> > >> Dave
> > >>
> > >> On Apr 15, 2011, at 8:14 AM, Leandro Hermida wrote:
> > >>
> > >>> Hi everyone,
> > >>>
> > >>> I was wondering what would be the way in Galaxy to program the
> following:
> > >>>
> > >>> - User clicks on a tool and form is displayed
> > >>> - They use a select multi menu in the form to pick lets say X
> multiple
> > >>> datasets from their history
> > >>> - When they click submit the tool launches X number of jobs in the
> history,
> > >>> on for each of the datasets selected.
> > >>>
> > >>> I have a common use case where users have to manually run the same
> tool over
> > >>> and over again with the same parameters for each dataset of interest
> in
> > >>> their histor

Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

[Leandro Hermida]

Hi again,

Sorry to maybe not understand how to get started, but I'm trying for
something even without the added complexity of a workflow.

If you could point me into the right direction: how would I have a single
tool where on the tool form there is a multi-select of certain datasets in
the user's history.  The user multi selects X datasets in the form and hits
submit and Galaxy will launch X tool jobs (on for each of the datasets) at
the same time in the history.

How do I go about doing this?

Sorry for being daft,
Leandro


On Tue, Apr 19, 2011 at 4:34 PM, Dave Walton  wrote:

> Is the server below down?  I'm trying to get there this morning and having
> no luck...
>
>
> https://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project#Loop_over_files
> _in_a_directory
>
> Dave
>
>
> On 4/15/11 12:16 PM, "Pieter Neerincx"  wrote:
>
> > Hi,
> >
> > You're not alone with this request! Unfortunately I wasn't able to join
> the
> > 2-day Galaxy Hackathon, but I heard from a colleague who just came back
> that
> > this was one of the topics they worked on. At the end of the hackathon
> they
> > had a working prototype:
> >
> >
> https://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project#Loop_over_files_i
> > n_a_directory
> >
> > Since they had only 2 days, it will need some polish, but I heard this
> hack
> > already made it into the development branch of Galaxy, so we may see
> something
> > like this in the near future :)
> >
> > Cheers,
> >
> > Pi
> >
> > On Apr 15, 2011, at 4:28 PM, Dave Walton wrote:
> >
> >> I've essentially asked the same question of the list in the past and
> gotten
> >> no real response.
> >>
> >> I have the same interest, but from a workflow perspective.
> >>
> >> * A module that allows me to select multiple datafiles (say fastq files)
> >> * Then pass each data file to a separate instance of a workflow that
> runs
> >> tophat and cufflinks
> >> * then another module that takes the final outputs of each of the
> workflow
> >> runs and sends them to a final module that merges results.
> >>
> >> I am attempting to implement something like this using the API, though
> the
> >> API is still pretty green from my perspective.
> >>
> >> I think functionality like this built into the workflow editor would be
> a
> >> great addition.
> >>
> >> Dave
> >>
> >> On Apr 15, 2011, at 8:14 AM, Leandro Hermida wrote:
> >>
> >>> Hi everyone,
> >>>
> >>> I was wondering what would be the way in Galaxy to program the
> following:
> >>>
> >>> - User clicks on a tool and form is displayed
> >>> - They use a select multi menu in the form to pick lets say X multiple
> >>> datasets from their history
> >>> - When they click submit the tool launches X number of jobs in the
> history,
> >>> on for each of the datasets selected.
> >>>
> >>> I have a common use case where users have to manually run the same tool
> over
> >>> and over again with the same parameters for each dataset of interest in
> >>> their history.  I would be great to be able programmatically or
> otherwise
> >>> with Galaxy to be able to use one form and multi select the datasets
> and
> >>> then launch the parallel jobs in one go.
> >>>
> >>> regards,
> >>> Leandro
> >>>
> >>> 
> >>
> >>
> >> ___
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> >> in your mail client.  To manage your subscriptions to this
> >> and other Galaxy lists, please use the interface at:
> >>
> >>  http://lists.bx.psu.edu/
> >
> > -
> > mobile: +31 6 143 66 783
> > e-mail: pieter.neeri...@gmail.com
> > skype:  pieter.online
> > -
> >
>
>
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Re: [galaxy-dev] Getting tool dirpath in a Python code file

[Leandro Hermida]

On Fri, Apr 15, 2011 at 7:27 PM, Peter Cock wrote:

> On Thu, Apr 14, 2011 at 2:56 PM, Leandro Hermida
>  wrote:
> > On Thu, Apr 14, 2011 at 3:17 PM, Peter Cock 
> > wrote:
> >>
> >> For standard Python tools in Galaxy, I'm using
> >> os.path.split(sys.argv[0])[0]
> >> to get the path, which on reflection probably should be written as
> >> os.path.dirname(sys.argv[0]) as you suggest.
> >>
> >> What do __file__ and sys.argv[0] give you? The simplest way to debug
> >> this is to add a print statement, since Galaxy will show the stdout.
> >>
> >
> > Hi Peter,
> >
> > __file__ throws an error: global name '__file__' is not defined
>
> I guess the script is being loaded as a string, and run with eval(...)
> or something like that. It would also explain why sys.argv[0] would
> be one of the Galaxy script files.
>
> > os.path.abspath(os.path.dirname(sys.argv[0])) gives me
> > /path/to/galaxy/scripts directory which is two levels up from what the
> tool
> > directory I want for example /path/to/galaxy/tools/mytool
>
> So combine that with ../tools/mytool/ and you're done? OK, you have
> to know the name of the folder your tool *should* be in... so not a
> perfect solution.


Thanks Peter, yes that's the same idea I did as a quick fix also don't
like the fact that my tool directory is hard-coded but oh well.  There must
be a way within Python in Galaxy importing something from Galaxy that has
the current tool directory path, it would seem that Galaxy needs to know
this and would store it anyway?

best,
Leandro
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Re: [galaxy-dev] Getting tool dirpath in a Python code file

[Leandro Hermida]

Hi sorry to ping again, but do any of the Galaxy developers have
advice/recommended approach for the problem in this thread?

On Thu, Apr 14, 2011 at 3:56 PM, Leandro Hermida  wrote:

> On Thu, Apr 14, 2011 at 3:17 PM, Peter Cock wrote:
>
>> On Thu, Apr 14, 2011 at 2:08 PM, Leandro Hermida
>>  wrote:
>> > Hi,
>> >
>> > I have a tool with a  tag and in that code
>> file
>> > I'm trying to get the tool dirpath where that script and the tool XML
>> > exist.  I've tried:
>> >
>> > os.path.abspath(os.path.dirname(sys.argv[0]))
>> > os.path.abspath(os.path.dirname(__file__))
>> >
>> > And both don't work as expected. Is there a galaxy class I could import
>> > which will have the tool directory path?
>> >
>> > regards,
>> > Leandro
>>
>> For standard Python tools in Galaxy, I'm using
>> os.path.split(sys.argv[0])[0]
>> to get the path, which on reflection probably should be written as
>> os.path.dirname(sys.argv[0]) as you suggest.
>>
>> What do __file__ and sys.argv[0] give you? The simplest way to debug
>> this is to add a print statement, since Galaxy will show the stdout.
>>
>>
> Hi Peter,
>
> __file__ throws an error: global name '__file__' is not defined
> os.path.abspath(os.path.dirname(sys.argv[0])) gives me
> /path/to/galaxy/scripts directory which is two levels up from what the tool
> directory I want for example /path/to/galaxy/tools/mytool
>
> Isn't there some Galaxy class I can import? I remember seeing in other code
> files "import galaxy" and would this have somewhere in it the current tool
> directory?
>
> -Leandro
>
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Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

[Leandro Hermida]

Hi Dave,

Thanks for the feedback, this to me would be a very useful feature to be
able to spawn multiple same jobs or workflows from one tool form using
different input datasets selected with multi select and all other form
parameters being the same.

Where are the docs and information for the Galaxy API? Wondering if I could
program this exact functionality in the script that the tool would execute.

thanks,
Leandro

On Fri, Apr 15, 2011 at 4:28 PM, Dave Walton  wrote:

> I've essentially asked the same question of the list in the past and gotten
> no real response.
>
> I have the same interest, but from a workflow perspective.
>
> * A module that allows me to select multiple datafiles (say fastq files)
> * Then pass each data file to a separate instance of a workflow that runs
> tophat and cufflinks
> * then another module that takes the final outputs of each of the workflow
> runs and sends them to a final module that merges results.
>
> I am attempting to implement something like this using the API, though the
> API is still pretty green from my perspective.
>
> I think functionality like this built into the workflow editor would be a
> great addition.
>
> Dave
>
> On Apr 15, 2011, at 8:14 AM, Leandro Hermida wrote:
>
> > Hi everyone,
> >
> > I was wondering what would be the way in Galaxy to program the following:
> >
> > - User clicks on a tool and form is displayed
> > - They use a select multi menu in the form to pick lets say X multiple
> datasets from their history
> > - When they click submit the tool launches X number of jobs in the
> history, on for each of the datasets selected.
> >
> > I have a common use case where users have to manually run the same tool
> over and over again with the same parameters for each dataset of interest in
> their history.  I would be great to be able programmatically or otherwise
> with Galaxy to be able to use one form and multi select the datasets and
> then launch the parallel jobs in one go.
> >
> > regards,
> > Leandro
> >
> > 
>
>
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[galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

[Leandro Hermida]

Hi everyone,

I was wondering what would be the way in Galaxy to program the following:

- User clicks on a tool and form is displayed
- They use a select multi menu in the form to pick lets say X multiple
datasets from their history
- When they click submit the tool launches X number of jobs in the history,
on for each of the datasets selected.

I have a common use case where users have to manually run the same tool over
and over again with the same parameters for each dataset of interest in
their history.  I would be great to be able programmatically or otherwise
with Galaxy to be able to use one form and multi select the datasets and
then launch the parallel jobs in one go.

regards,
Leandro
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Re: [galaxy-dev] Getting tool dirpath in a Python code file

[Leandro Hermida]

On Thu, Apr 14, 2011 at 3:17 PM, Peter Cock wrote:

> On Thu, Apr 14, 2011 at 2:08 PM, Leandro Hermida
>  wrote:
> > Hi,
> >
> > I have a tool with a  tag and in that code
> file
> > I'm trying to get the tool dirpath where that script and the tool XML
> > exist.  I've tried:
> >
> > os.path.abspath(os.path.dirname(sys.argv[0]))
> > os.path.abspath(os.path.dirname(__file__))
> >
> > And both don't work as expected. Is there a galaxy class I could import
> > which will have the tool directory path?
> >
> > regards,
> > Leandro
>
> For standard Python tools in Galaxy, I'm using
> os.path.split(sys.argv[0])[0]
> to get the path, which on reflection probably should be written as
> os.path.dirname(sys.argv[0]) as you suggest.
>
> What do __file__ and sys.argv[0] give you? The simplest way to debug
> this is to add a print statement, since Galaxy will show the stdout.
>
>
Hi Peter,

__file__ throws an error: global name '__file__' is not defined
os.path.abspath(os.path.dirname(sys.argv[0])) gives me
/path/to/galaxy/scripts directory which is two levels up from what the tool
directory I want for example /path/to/galaxy/tools/mytool

Isn't there some Galaxy class I can import? I remember seeing in other code
files "import galaxy" and would this have somewhere in it the current tool
directory?

-Leandro
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[galaxy-dev] Getting tool dirpath in a Python code file

[Leandro Hermida]

Hi,

I have a tool with a  tag and in that code file
I'm trying to get the tool dirpath where that script and the tool XML
exist.  I've tried:

os.path.abspath(os.path.dirname(sys.argv[0]))
os.path.abspath(os.path.dirname(__file__))

And both don't work as expected. Is there a galaxy class I could import
which will have the tool directory path?

regards,
Leandro
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[galaxy-dev] Automatically sending an email to users you've shared a history with

[Leandro Hermida]

Hi all,

Can Galaxy be configured to automatically send an email to users you have
shared a history with (with appropriate link to Galaxy history URL
included)?  I tried to search the mail list history and could not find,
which bring another question, is Google the only way to search the galaxy
mailing list archive?

regards,
Leandro
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Re: [galaxy-dev] MySQL to PostgreSQL migration scripts available here

[Leandro Hermida]

Hi Louise,

Sorry if this is a bad recommendation and if you already tried it and it
doesn't work for Galaxy, but did you know that the MySQL database dump
program mysqldump has a feature to dump the entire database properly for
import into PostgreSQL?

mysqldump --compatible=postgresql [galaxy db name] > galaxy.sql

regards,
Leandro

2011/4/11 Louise-Amélie Schmitt 

> Hello everyone
>
> I finally managed to finish my two scripts. It's kind of dirty coded
> (I'm not a Perl fan + I was in a hurry), but at least they worked for
> me. I could successfully transfer the data from an old MySQL Galaxy to
> my new PSQL Galaxy.
>
> Before running the scripts, you should already have run your new Galaxy
> instance so that the tables are properly created. Please note that the
> scripts will erase everything the target database might contain. It's
> aimed to make a 'clone' of the old database, not to merge both.
>
> Here is how to do the transfer:
>
> Requirements: DBD::mysql and DBD:Pg Perl modules
>
> 1: run galaxy-My2Pg.pl with the appropriate arguments (see the comments
> in the script's first lines)
>
> 2: start your Galaxy instance
>
> If the galaxy instance starts without throwing a fit, you can probably
> stop here. (I didn't have that chance though)
>
> Otherwise you most certainly have the wrong database version:
>
> 3: run sh manage_db.sh upgrade (to get the version right)
>
> 4: run galaxy-My2Pg_fix-seq.pl with the appropriate arguments blah, it
> will set the sequences at the right number since manage_db.sh seems to
> mess them up.
>
> Please note that even if it might work for some other databases, it was
> only tested on Galaxy, and I decline any responsibility if it doesn't
> work, throws data trhough the windows or blows your whole office up. You
> should back your data up beforehand in any case.
>
> Cheers,
> LA
>
> ___
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> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
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[galaxy-dev] Does REMOTE_USER have to be an email address?

[Leandro Hermida]

Hello,

When returning REMOTE_USER env var from the external authentication method
does it have to be an email address for Galaxy? The docs aren't very clear
on that, in the main External Authentication section it says you have to
have to set remote_user_maildomain if you aren't return an email address
(and the domain will be appended it seems) but in the mod_authnz_ldap
section it says you are allowed to set any attribute to return as
REMOTE_USER.

regards,
Leandro
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Re: [galaxy-dev] reason/advantages for making Galaxy proxy using mod_rewrite instead of mod_proxy

[Leandro Hermida]

Sorry one more question... are these lines in the Galaxy wiki instructions
still correct for the latest galaxy-dist?

RewriteRule ^/galaxy/static/style/(.*)
/home/nate/galaxy_dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*)
/home/nate/galaxy_dist/static/scripts/packed/$1 [L]

best,
Leandro

On Fri, Apr 8, 2011 at 1:55 PM, Leandro Hermida
wrote:

> Hi again,
>
> After a bit more research I guess I can see why -- since as you show in the
> instructions you also intend to serve static content via the proxy server
> and this requires using mod_rewrite anyway that you chose to do the reverse
> proxy part also using mod_rewrite.  Sorry for being confused, I have seen
> before configurations with mod_proxy and mod_rewrite directives together
> doing the same thing I was wondering why! :)
>
> best,
> Leandro
>
>
> On Fri, Apr 8, 2011 at 12:22 PM, Leandro Hermida <
> soft...@leandrohermida.com> wrote:
>
>> Hi all,
>>
>> Sorry if this question has been asked before searched and couldn't find
>> anyone specifically talking about this.  In the Galaxy wiki under
>> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy there
>> are instructions for setting up Galaxy behind a web server proxy.  I
>> wondered what are the reasons/advantages of doing a reverse proxy using all
>> mod_rewrite directives (as shown in the instructions) vs doing a standard
>> Apache front-end reverse proxy:
>>
>> ProxyRequests Off
>> ProxyPass / http://galaxy.host.domain:8080/
>> ProxyPassReverse / http://galaxy.host.domain:8080/
>>
>> The instructions using mod_rewrite are making a reverse proxy too since
>> the RewriteRule directive has the [P] flag.
>>
>> regards,
>> Leandro
>>
>
>
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Re: [galaxy-dev] reason/advantages for making Galaxy proxy using mod_rewrite instead of mod_proxy

[Leandro Hermida]

Hi again,

After a bit more research I guess I can see why -- since as you show in the
instructions you also intend to serve static content via the proxy server
and this requires using mod_rewrite anyway that you chose to do the reverse
proxy part also using mod_rewrite.  Sorry for being confused, I have seen
before configurations with mod_proxy and mod_rewrite directives together
doing the same thing I was wondering why! :)

best,
Leandro

On Fri, Apr 8, 2011 at 12:22 PM, Leandro Hermida  wrote:

> Hi all,
>
> Sorry if this question has been asked before searched and couldn't find
> anyone specifically talking about this.  In the Galaxy wiki under
> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy there
> are instructions for setting up Galaxy behind a web server proxy.  I
> wondered what are the reasons/advantages of doing a reverse proxy using all
> mod_rewrite directives (as shown in the instructions) vs doing a standard
> Apache front-end reverse proxy:
>
> ProxyRequests Off
> ProxyPass / http://galaxy.host.domain:8080/
> ProxyPassReverse / http://galaxy.host.domain:8080/
>
> The instructions using mod_rewrite are making a reverse proxy too since the
> RewriteRule directive has the [P] flag.
>
> regards,
> Leandro
>
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[galaxy-dev] reason/advantages for making Galaxy proxy using mod_rewrite instead of mod_proxy

[Leandro Hermida]

Hi all,

Sorry if this question has been asked before searched and couldn't find
anyone specifically talking about this.  In the Galaxy wiki under
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy there
are instructions for setting up Galaxy behind a web server proxy.  I
wondered what are the reasons/advantages of doing a reverse proxy using all
mod_rewrite directives (as shown in the instructions) vs doing a standard
Apache front-end reverse proxy:

ProxyRequests Off
ProxyPass / http://galaxy.host.domain:8080/
ProxyPassReverse / http://galaxy.host.domain:8080/

The instructions using mod_rewrite are making a reverse proxy too since the
RewriteRule directive has the [P] flag.

regards,
Leandro
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