- galaxy-dev - lists.galaxyproject.org

tool shed updates broken on my local server
by Anne Pajon 06 Feb '15

06 Feb '15

Hi there, I am currently trying to migrate our Galaxy production server onto new hardware and I am facing many challenges. Recently I've been unable to update tools from the tool shed. During the migration I've moved across the files, the data, the tools and their dependencies as well as the database. But I am getting this error while trying to update any tools that are marked 'Updates are available in the Tool Shed for this revision' from the GUI: Admin > Manage installed tool shed repositories > fasta_formatter menu Get updates: Internal Server Error Galaxy was unable to successfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. Here is the log from paster.log: 10.20.13.16 - - [29/Jan/2015:16:43:45 +0100] "GET /admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=fasta_formatter&owner=devteam&changeset_revision=8f0ae92440b8&latest_changeset_revision=1dbb5181c327&latest_ctx_rev=1 HTTP/1.1" 500 - "http://bioinf-gal001:8080/admin_toolshed/browse_repositories?async=false&so…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:35.0) Gecko/20100101 Firefox/35.0" Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'get' URL: http://bioinf-gal001:8080/admin_toolshed/update_to_changeset_revision?tool_… File '/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/mnt/nfs/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/mnt/nfs/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 87 in decorator return func( self, trans, *args, **kwargs ) File '/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1953 in update_to_changeset_revision persist=True ) File '/mnt/nfs/data/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py', line 31 in __init__ metadata_dict=metadata_dict, user=None ) File '/mnt/nfs/data/galaxy/galaxy-dist/lib/tool_shed/metadata/metadata_generator.py', line 60 in __init__ self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) } AttributeError: 'NoneType' object has no attribute 'get' CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5' HTTP_CONNECTION: 'keep-alive' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a44ec9cad39b01202307c62c9a25600e232d5d3d597344cb74ba4cd8a7123f6e9' HTTP_HOST: 'bioinf-gal001:8080' HTTP_REFERER: 'http://bioinf-gal001:8080/admin_toolshed/browse_repositories?async=false&so…' HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:35.0) Gecko/20100101 Firefox/35.0' PATH_INFO: '/admin_toolshed/update_to_changeset_revision' QUERY_STRING: 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=fasta_formatter&owner=de…' REMOTE_ADDR: '10.20.13.16' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x7f34f7a50590> is_api_request: False paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a44ec9cad39b01202307c62c9a25600e232d5d3d597344cb74ba4cd8a7123f6e9'>, 'galaxysession=c6ca0ddb55be603a44ec9cad39b01202307c62c9a25600e232d5d3d597344cb74ba4cd8a7123f6e9') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x7f34f7a50550> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x7f34f76ef1d0> paste.parsed_querystring: ([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('name', 'fasta_formatter'), ('owner', 'devteam'), ('changeset_revision', '8f0ae92440b8'), ('latest_changeset_revision', '1dbb5181c327'), ('latest_ctx_rev', '1')], 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=fasta_formatter&owner=de…') paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: 'fdaf9004a7d511e49d63005056a77528' webob._parsed_query_vars: (MultiDict([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('name', 'fasta_formatter'), ('owner', 'devteam'), ('changeset_revision', '8f0ae92440b8'), ('latest_changeset_revision', '1dbb5181c327'), ('latest_ctx_rev', '1')]), 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=fasta_formatter&owner=de…') wsgi process: 'Multithreaded' ------------------------------------------------------------ Anything obvious that I've missed? Many thanks in advance for your help. Kind regards, Anne. -- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon(a)cruk.cam.ac.uk | +44 (0)1223 769 631

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Bug? Uploaded files not adding to history (Nginx upload)
by Federico Zambelli 06 Feb '15

06 Feb '15

Hi everybody, I have recently updated our lab Galaxy instance to the latest stable latest_2015.01.13. I have now a problem with uploaded files: they are not added to history. The problem disappears if I disable the nginx upload feature (that worked just fine until the update). Maybe it is of help to know that the files are correctly uploaded to the "nginx_upload_store" directory configured in galaxy.ini but then they are not added to the current history. Best, Federico Z.

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parallesim
by Roberto Alonso CIPF 06 Feb '15

06 Feb '15

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 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 AS history_dataset_association_name, 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 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 = history_dataset_association.dataset_id \nWHERE 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: ralonso(a)cipf.es

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Re: [galaxy-dev] galaxy report page - server error solution?
by Fernandez Edgar 06 Feb '15

06 Feb '15

Actually, here's what I came up with : diff users.py ARCHIVES/users.py_20150205_9.28.18 23c23 < q = sa.select( ( sa.func.date( galaxy.model.User.table.c.create_time ).label( 'date' ), --- > q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( galaxy.model.User.table.c.create_time ) ).label( 'date' ), 26c26 < group_by = [ sa.func.year ( galaxy.model.User.table.c.create_time ), sa.func.month ( galaxy.model.User.table.c.create_time ) ], --- > group_by = [ sa.func.date_trunc( 'month', sa.func.date( galaxy.model.User.table.c.create_time ) ) ], 48c48 < q = sa.select( ( sa.func.date( galaxy.model.User.table.c.create_time ).label( 'date' ), --- > q = sa.select( ( sa.func.date_trunc( 'day', sa.func.date( galaxy.model.User.table.c.create_time ) ).label( 'date' ), 53c53 < group_by = [ sa.func.day( sa.func.date( galaxy.model.User.table.c.create_time ) ) ], --- > group_by = [ sa.func.date_trunc( 'day', sa.func.date( galaxy.model.User.table.c.create_time ) ) ], 79c79 < q = sa.select( ( sa.func.date( galaxy.model.User.table.c.create_time ).label( 'date' ), --- > q = sa.select( ( sa.func.date_trunc( 'day', sa.func.date( galaxy.model.User.table.c.create_time ) ).label( 'date' ), diff jobs.py ARCHIVES/jobs.py_20150205_9.28.22 282c282 < jobs_by_month = sa.select( ( sa.func.date( model.Job.table.c.create_time ).label( 'date' ), --- > jobs_by_month = sa.select( ( sa.func.date_trunc( 'month', model.Job.table.c.create_time ).label( 'date' ), 315c315 < jobs_in_error_by_month = sa.select( ( sa.func.date( model.Job.table.c.create_time ).label( 'date' ), --- > jobs_in_error_by_month = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ).label( 'date' ), 320c320 < group_by=[ sa.func.year ( model.Job.table.c.create_time ), sa.func.month ( sa.func.date( model.Job.table.c.create_time ) ) ], --- > group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ) ], 364c364 < q = sa.select( ( sa.func.date( model.Job.table.c.create_time ).label( 'date' ), --- > q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ).label( 'date' ), 371c371 < group_by=[ sa.func.year ( model.Job.table.c.create_time ), sa.func.month ( sa.func.date( model.Job.table.c.create_time ) ) ], --- > group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ) ], 420c420 < q = sa.select( ( sa.func.date( model.Job.table.c.create_time ).label( 'date' ), --- > q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ).label( 'date' ), 425c425 < group_by=[ sa.func.year ( model.Job.table.c.create_time ), sa.func.month ( sa.func.date( model.Job.table.c.create_time ) ) ], --- > group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ) ], Let me know what you think!!! Cordialement / Regards, Edgar Fernandez De : Fernandez Edgar Envoyé : February-05-15 9:49 AM À : 'galaxy-dev(a)bx.psu.edu' Objet : galaxy report page - server error solution? Hello guys, So I've been working on the Galaxy report page. It works fine however I'm using MySQL and I'm getting some server errors on some webpages. I found the solution: https://lists.galaxyproject.org/pipermail/galaxy-dev/2009-August/000641.html But can some please confirm the following: 1. The location of the files users.py and jobs.py is /home/galaxy/galaxy-prod/lib/galaxy/webapps/reports/controllers 2. There is three (3) "select closes" using five (5) "date_trunc" functions in users.py. 3. There is eight (8) "select closes" using fourteen (4) "date_trunc" functions in jobs.py. 4. Here is an example of what I can come up with. Is it correct? · WRONG: jobs_in_error_by_month = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ).label( 'date' ), sa.func.count( model.Job.table.c.id ).label('total_jobs' ) ), whereclause=sa.and_ ( model.Job.table.c.state == 'error', model.Job.table.c.user_id != monitor_user_id ), from_obj=[ model.Job.table ], group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ) ], order_by=[ sa.desc( 'date' ) ] ) · RIGHT: jobs_in_error_by_month = sa.select( ( sa.func.count( model.Job.table.c.id ).label('total_jobs' ) ), whereclause=sa.and_ ( model.Job.table.c.state == 'error', model.Job.table.c.user_id != monitor_user_id ), from_obj=[ model.Job.table ], group_by=[ day(model.Job.table.c.create_time), month(model.Job.table.c.create_time), year(model.Job.table.c.create_time) ], order_by=[ sa.desc( 'date' ) ] ) Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218

3 4

parallelism
by Roberto Alonso 05 Feb '15

05 Feb '15

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 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 AS history_dataset_association_name, 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 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 = history_dataset_association.dataset_id \nWHERE 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

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galaxy report page - server error solution?
by Fernandez Edgar 05 Feb '15

05 Feb '15

Hello guys, So I've been working on the Galaxy report page. It works fine however I'm using MySQL and I'm getting some server errors on some webpages. I found the solution: https://lists.galaxyproject.org/pipermail/galaxy-dev/2009-August/000641.html But can some please confirm the following: 1. The location of the files users.py and jobs.py is /home/galaxy/galaxy-prod/lib/galaxy/webapps/reports/controllers 2. There is three (3) "select closes" using five (5) "date_trunc" functions in users.py. 3. There is eight (8) "select closes" using fourteen (4) "date_trunc" functions in jobs.py. 4. Here is an example of what I can come up with. Is it correct? · WRONG: jobs_in_error_by_month = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ).label( 'date' ), sa.func.count( model.Job.table.c.id ).label('total_jobs' ) ), whereclause=sa.and_ ( model.Job.table.c.state == 'error', model.Job.table.c.user_id != monitor_user_id ), from_obj=[ model.Job.table ], group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ) ], order_by=[ sa.desc( 'date' ) ] ) · RIGHT: jobs_in_error_by_month = sa.select( ( sa.func.count( model.Job.table.c.id ).label('total_jobs' ) ), whereclause=sa.and_ ( model.Job.table.c.state == 'error', model.Job.table.c.user_id != monitor_user_id ), from_obj=[ model.Job.table ], group_by=[ day(model.Job.table.c.create_time), month(model.Job.table.c.create_time), year(model.Job.table.c.create_time) ], order_by=[ sa.desc( 'date' ) ] ) Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218

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Tools to download SRA datasets from GEO
by Ryan G 05 Feb '15

05 Feb '15

Do any tools exist to download GEO datasets from NCBI?

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binaries version tracking
by Philippe Moncuquet 04 Feb '15

04 Feb '15

Hi, I would like to know how developers of Galaxy instances are keeping track of binaries version. I know how to check for the installed tools and their different revisions numbers, there is also the workflow version tracking that will let you know when something has been updated but how to keep track of the binaries used by wrappers ? Is there something in Galaxy that I am not aware of or are you using external solution ? Regards, Philip

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Starting uWSGI
by Nicholas Kline 04 Feb '15

04 Feb '15

Hello, I am trying to setup a local production Galaxy server for our department. Our Galaxy server environment is as follows: - Ubuntu 14.04 64-bit - 94 GB Memory - Intel Xeon - Python virtual environment - Nginx - PostgreSQL - ProFTPd Today I tried starting the Galaxy server for the first time. I think the first step in that process is starting uWSGI, correct? To do so, I executed these commands: cd ~/galaxy-dist/ PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste config/galaxy.ini However, it appears something failed. This information is returned: The program 'uwsgi' can be found in the following packages: * uwsgi-core * uwsgi-plugin-alarm-curl * uwsgi-plugin-alarm-xmpp * uwsgi-plugin-curl-cron * uwsgi-plugin-emperor-pg * uwsgi-plugin-erlang * uwsgi-plugin-geoip * uwsgi-plugin-graylog2 * uwsgi-plugin-jvm-openjdk-6 * uwsgi-plugin-jvm-openjdk-7 * uwsgi-plugin-ldap * uwsgi-plugin-lua5.1 * uwsgi-plugin-lua5.2 * uwsgi-plugin-php * uwsgi-plugin-psgi * uwsgi-plugin-python * uwsgi-plugin-python3 * uwsgi-plugin-rack-ruby1.9.1 * uwsgi-plugin-router-access * uwsgi-plugin-sqlite3 * uwsgi-plugin-v8 * uwsgi-plugin-xslt Ask your administrator to install one of them According to the galaxy documentation at https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling , "uWSGI support is built in to nginx, so no extra modules or recompiling should be required". Also, should '--ini-paste config/galaxy.ini' really be configured like this instead: --ini-paste universe_wsgi.ini ? Thank you

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Tool Tests failing with "Exception: History in error state."
by Peter Cock 04 Feb '15

04 Feb '15

Retitling thread, On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote: > Thanks Dave, > > The good news is yes, the tests are running again on the > Test Tool Shed (although not the main Tool Shed yet), and > many of my tools now have successful test results from > last night. > > e.g. My new basic mummer tool which now has a full set > of dependency packages thanks to Bjoern: > https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer > > The bad news is there are many unexpected failures with: > "Exception: History in error state." > > I'm sure you'll learn more once you look over the logs, > > Thank you, > > Peter Right now the mummer example given above is passing, but I am still getting this error on some of my tools, e.g. https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go tested 2015-01-25 11:21:12 https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss tested 2015-01-25 10:52:03 (Many of my other tools are also currently listed with different unexpected failures, some of which include the "Exception: History in error state." traceback.) Interestingly, I've just got what appears to be the same exception from a TravisCI test run (following a trivial change to README files): https://travis-ci.org/peterjc/galaxy_blast/builds/48893916 e.g. (one of many similar failing tests in this log) ====================================================================== ERROR: test_tool_000000 (functional.test_toolbox.TestForTool_blastxml_to_top_descr) BLAST top hit descriptions ( blastxml_to_top_descr ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py", line 268, in test_tool self.do_it( td ) File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py", line 37, in do_it stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py", line 42, in stage_data_in_history upload_wait() File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py", line 279, in wait while not self.__history_ready( history_id ): File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py", line 297, in __history_ready return self._state_ready( state, error_msg="History in error state." ) File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py", line 356, in _state_ready raise Exception( error_msg ) Exception: History in error state. I do not recall seeing this problem locally when using my development instllation of galaxy-central. The TravisCI failure suggests this could be a stochastic resource contention (I can re-run the TravisCI build and see if this works second time round?), which is more prone to fail under the Tool Shed framework? Peter

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