Hello,

I am using the galaxy built-in database,  SQLAlchemy on top of sql lite?
May I swith to postgress?

Regards

On 5 February 2015 at 14:41, Hans-Rudolf Hotz <h...@fmi.ch> wrote:

> Hi Roberto
>
> just double checking: are you using a PostgreSQL database, or are you
> relying on the built in SQLite?
>
> Hans-Rudolf
>
>
>
> On 02/05/2015 02:26 PM, Roberto Alonso CIPF wrote:
>
>>
>> Hello,
>>
>> I am trying to use parallelism in Galaxy.  I added this entry to the
>> tool xml config:
>>
>> <tool id="fa_gc_content_1" name="Compute GC content">
>>    <description>for each sequence in a file</description>
>>    <parallelism method="basic" split_size="8"
>> split_mode="number_of_parts"></parallelism>
>>
>>
>> But when I run the job, the log shows the next:
>>
>>
>>
>> Traceback (most recent call last):
>>    File "/home/ralonso/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
>> line 158, in prepare_job
>>      job_wrapper.prepare()
>>    File "/home/ralonso/galaxy-dist/lib/galaxy/jobs/__init__.py", line
>> 1607, in prepare
>>      tool_evaluator.set_compute_environment( compute_environment )
>>    File "/home/ralonso/galaxy-dist/lib/galaxy/tools/evaluation.py", line
>> 53, in set_compute_environment
>>      incoming = self.tool.params_from_strings( incoming, self.app )
>>    File "/home/ralonso/galaxy-dist/lib/galaxy/tools/__init__.py", line
>> 2810, in params_from_strings
>>      return params_from_strings( self.inputs, params, app, ignore_errors )
>>    File
>> "/home/ralonso/galaxy-dist/lib/galaxy/tools/parameters/__init__.py",
>> line 103, in params_from_strings
>>      value = params[key].value_from_basic( value, app, ignore_errors )
>>    File
>> "/home/ralonso/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
>> 162, in value_from_basic
>>      return self.to_python( value, app )
>>    File
>> "/home/ralonso/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
>> 1999, in to_python
>>      return app.model.context.query( app.model.HistoryDatasetAssociation
>> ).get( int( value ) )
>>    File
>> "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-
>> linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>> line 775, in get
>>      return self._load_on_ident(key)
>>    File
>> "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-
>> linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>> line 2512, in _load_on_ident
>>      return q.one()
>>    File
>> "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-
>> linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>> line 2184, in one
>>      ret = list(self)
>>    File
>> "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-
>> linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>> line 2227, in __iter__
>>      return self._execute_and_instances(context)
>>    File
>> "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-
>> linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>> line 2242, in _execute_and_instances
>>      result = conn.execute(querycontext.statement, self._params)
>>    File
>> "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-
>> linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>> line 1449, in execute
>>      params)
>>    File
>> "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-
>> linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>> line 1584, in _execute_clauseelement
>>      compiled_sql, distilled_params
>>    File
>> "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-
>> linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>> line 1698, in _execute_context
>>      context)
>>    File
>> "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-
>> linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>> line 1691, in _execute_context
>>      context)
>>    File
>> "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-
>> linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
>> line 331, in do_execute
>>      cursor.execute(statement, parameters)
>> OperationalError: (OperationalError) database is locked u'SELECT
>> history_dataset_association.id <http://history_dataset_association.id>
>> AS history_dataset_association_id,
>> history_dataset_association.history_id AS
>> history_dataset_association_history_id,
>> history_dataset_association.dataset_id AS
>> history_dataset_association_dataset_id,
>> history_dataset_association.create_time AS
>> history_dataset_association_create_time,
>> history_dataset_association.update_time AS
>> history_dataset_association_update_time,
>> history_dataset_association.state AS history_dataset_association_state,
>> history_dataset_association.copied_from_history_dataset_association_id
>> AS
>> history_dataset_association_copied_from_history_dataset_association_id,
>> history_dataset_association.copied_from_library_dataset_
>> dataset_association_id
>> AS
>> history_dataset_association_copied_from_library_dataset_
>> dataset_association_id,
>> history_dataset_association.hid AS history_dataset_association_hid,
>> history_dataset_association.name
>> <http://history_dataset_association.name> AS
>> history_dataset_association_name, history_dataset_association.info
>> <http://history_dataset_association.info> AS
>> history_dataset_association_info, history_dataset_association.blurb AS
>> history_dataset_association_blurb, history_dataset_association.peek AS
>> history_dataset_association_peek,
>> history_dataset_association.tool_version AS
>> history_dataset_association_tool_version,
>> history_dataset_association.extension AS
>> history_dataset_association_extension,
>> history_dataset_association.metadata AS
>> history_dataset_association_metadata,
>> history_dataset_association.parent_id AS
>> history_dataset_association_parent_id,
>> history_dataset_association.designation AS
>> history_dataset_association_designation,
>> history_dataset_association.deleted AS
>> history_dataset_association_deleted, history_dataset_association.purged
>> AS history_dataset_association_purged,
>> history_dataset_association.visible AS
>> history_dataset_association_visible,
>> history_dataset_association.hidden_beneath_collection_instance_id AS
>> history_dataset_association_hidden_beneath_collection_instance_id,
>> history_dataset_association.extended_metadata_id AS
>> history_dataset_association_extended_metadata_id, dataset_1.id
>> <http://dataset_1.id> AS dataset_1_id, dataset_1.create_time AS
>> dataset_1_create_time, dataset_1.update_time AS dataset_1_update_time,
>> dataset_1.state AS dataset_1_state, dataset_1.deleted AS
>> dataset_1_deleted, dataset_1.purged AS dataset_1_purged,
>> dataset_1.purgable AS dataset_1_purgable, dataset_1.object_store_id AS
>> dataset_1_object_store_id, dataset_1.external_filename AS
>> dataset_1_external_filename, dataset_1._extra_files_path AS
>> dataset_1__extra_files_path, dataset_1.file_size AS dataset_1_file_size,
>> dataset_1.total_size AS dataset_1_total_size, dataset_1.uuid AS
>> dataset_1_uuid \nFROM history_dataset_association LEFT OUTER JOIN
>> dataset AS dataset_1 ON dataset_1.id <http://dataset_1.id> =
>> history_dataset_association.dataset_id \nWHERE
>> history_dataset_association.id <http://history_dataset_association.id> =
>> ?' (1,)
>> galaxy.jobs.runners ERROR 2015-02-05 12:58:11,431 (89_486) Failure
>> preparing job
>>
>> So when one task tries to run it fails, it seems that the database is
>> locked by other task. When I run with 4 splits it never happen, but with
>> 5 it begins to happen. Indeed with 5 splits sometimes it doesn't happen,
>> but since 6 it always occurs.
>>
>> Could you please help me?
>>
>>
>>
>> Regards
>>
>> --
>> Roberto Alonso
>> Functional Genomics Unit
>> Bioinformatics and Genomics Department
>> Prince Felipe Research Center (CIPF)
>> C./Eduardo Primo Yúfera (Científic), nº 3
>> (junto Oceanografico)
>> 46012 Valencia, Spain
>> Tel: +34 963289680 Ext. 1021
>> Fax: +34 963289574
>> E-Mail: ralo...@cipf.es <mailto:ralo...@cipf.es>
>>
>>
>> ___________________________________________________________
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>>
>>


-- 
Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(junto Oceanografico)
46012 Valencia, Spain
Tel: +34 963289680 Ext. 1021
Fax: +34 963289574
E-Mail: ralo...@cipf.es
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