February 2015 - galaxy-dev - lists.galaxyproject.org

gui and command line trouble
by Edlund, Anna 10 Feb '15

10 Feb '15

Hi there. I am trying to run MGTAXA to generate taxonomic predictions on assembled contigs in fasta format. I try to use both the gui at http://mgtaxa.jcvi.org/ with username aedlund@jcvi and 6926edlund(a)gmail.com. Both of these jobs have been running for days (they are yellow). When I try and use the standard command via the terminal nothing happens either. This command was working earlier for bacteria classification. Do you have any ideas of what I can do to use this tool? Thank you for your awesome help. Best, Anna

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"This job is waiting to run"
by Ryan G 06 Feb '15

06 Feb '15

I tried setting up Galaxy to use Sun Grid Engine, but failed miserably. I removed my config/job_conf.xml hoping Galaxy would revert to its default state, but jobs are no longer being dispatched. I don't see any errors in the log. How can I get Galaxy to 1) use SGE, or 2) revert to its default state for running jobs. The page, https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster isn't 100% clear on how to set up a simply configuration for SGE. I'd be happy to contribute mine as an example, if I can get it running.

2 2

backtrace -> bug?
by Langhorst, Brad 06 Feb '15

06 Feb '15

Is this a bug you want in trello? got this back trace when attempting to get updates to the picard tool 172.17.130.111 - - [06/Feb/2015:13:45:55 -0400] "POST /library_common/library_item_updates HTTP/1.0" 200 - "http://galaxy.neb.com/library_common/browse_library?sort=name&f-description…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.111 Safari/537.36" galaxy.tools.data WARNING 2015-02-06 13:45:57,640 Cannot find index file '/mnt/galaxy/data/galaxy/tmp/tmp-toolshed-gmfcr_ys2eZ/picard_index.loc' for tool data table 'picard_indexes' galaxy.tools.data DEBUG 2015-02-06 13:45:57,641 Loading another instance of data table 'picard_indexes', attempting to merge content. galaxy.tools.data DEBUG 2015-02-06 13:45:58,724 Loading another instance of data table 'picard_indexes', attempting to merge content. galaxy.tools.data DEBUG 2015-02-06 13:45:59,161 Loading another instance of data table 'picard_indexes', attempting to merge content. galaxy.tools.data DEBUG 2015-02-06 13:45:59,307 Loading another instance of data table 'picard_indexes', attempting to merge content. galaxy.tools.data DEBUG 2015-02-06 13:45:59,814 Loading another instance of data table 'picard_indexes', attempting to merge content. galaxy.tools.data DEBUG 2015-02-06 13:45:59,981 Loading another instance of data table 'picard_indexes', attempting to merge content. 172.17.130.111 - - [06/Feb/2015:13:46:00 -0400] "POST /library_common/library_item_updates HTTP/1.0" 200 - "http://galaxy.neb.com/library_common/browse_library?sort=name&f-description…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.111 Safari/537.36" galaxy.tools.data DEBUG 2015-02-06 13:46:01,205 Loading another instance of data table 'picard_indexes', attempting to merge content. galaxy.tools.data DEBUG 2015-02-06 13:46:01,380 Loading another instance of data table 'picard_indexes', attempting to merge content. 172.17.130.190 - - [06/Feb/2015:13:45:50 -0400] "GET /admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=picard&owner=devteam&changeset_revision=e0232cbac965&latest_changeset_revision=bf1c3f9f8282&latest_ctx_rev=3 HTTP/1.0" 500 - "http://galaxy.neb.com/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/39.0.2171.95 Safari/537.36" Error - <type 'exceptions.AttributeError'>: 'list' object has no attribute 'iteritems' URL: http://galaxy.neb.com/admin_toolshed/update_to_changeset_revision?tool_shed… File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/mnt/galaxy/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/galaxy/data/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 107 in __call__ return self.app( environ, start_response ) File '/mnt/galaxy/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/galaxy/data/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 87 in decorator return func( self, trans, *args, **kwargs ) File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1954 in update_to_changeset_revision irmm.generate_metadata_for_changeset_revision() File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/tool_shed/metadata/metadata_generator.py', line 443 in generate_metadata_for_changeset_revision metadata_dict ) File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/tool_shed/metadata/metadata_generator.py', line 648 in generate_tool_metadata for param_name, values in ttb.inputs.iteritems(): AttributeError: 'list' object has no attribute 'iteritems'

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galaxy of dm6
by Jian Lu 06 Feb '15

06 Feb '15

Hi folks, I wonder when you guys will include the newly updated genome assembly of Drosophila melanogaster (dm6) and the corresponding multiple alignments into the galaxy webserver. Best, Jian Lu -- Jian Lu, Ph. D. Principal Investigator Center for Life Sciences (CLS) Center of Bioinformatics State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing, China, 100871 http://evolution-pku.org/

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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 05 Feb '15

05 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

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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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