- galaxy-dev - lists.galaxyproject.org

set up an asynchronous data source in galaxy
by SAPET, Frederic 26 Aug '19

26 Aug '19

Hi, I'm trying to set up an asynchronous data source in galaxy. I follow the examples that Helena provide here : https://github.com/erasche/galaxy-data_source-examples/tree/master/flask It's a success for synchronous modE. But when I test the asynchronous mode, it fails. from what I understand, the file in history (that would contains the data) is not well created. The example creates a link like this one : https://galaxydev.biogemma.fr:4430/export/?gx_url=https%3A%2F%2Fgalaxydev.b… When I click on the link, no file is created in my history. The error in the log is : File "lib/galaxy/webapps/galaxy/controllers/async.py", line 150, in index open(data.file_name, 'wb').close() # create the file IOError: [Errno 2] No such file or directory: '' The filename is missing, so I have no new file in my history waiting for the asynchronous process to fill it. I've described the error here (with complete log messages) : https://github.com/erasche/galaxy-data_source-examples/issues/6 Can anybody reproduce this? Is this an issue? or a misconfiguration from my side? thank you. Fred

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upload issues with gff3.gz files.
by SAPET, Frederic 26 Aug '19

26 Aug '19

Hi, I'm using bioblend to populate a library in galaxy. it's work well (bam and vcf). But I have issues with some gff3.gz files. For few of them (over 40 files) I see errors in the log. If I upload that file (that fails with bioblend) it works using the upload tool on the interface. It's auto-detected as "tabular". I can then change datatype to gff3.gz. It works (with a little issue, the file is described as: 1 line, 41,085 comments. That's not true, there is not comments in my file). If I upload that file using the upload tool on the interface, it will fail if I set the datatype to gff3.gz during the upload process. I see then the same type of error (as I see with my bioblend script). I need some ideas, do you have tips ? Maybe some clues to follow... thank you. error type is : Traceback (most recent call last): File "lib/galaxy/jobs/runners/__init__.py", line 510, in _finish_or_resubmit_job job_wrapper.finish(tool_stdout, tool_stderr, exit_code, check_output_detected_state=check_output_detected_state, job_stdout=job_stdout, job_stderr=job_stderr) File "lib/galaxy/jobs/__init__.py", line 1428, in finish self.sa_session.flush() File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/orm/scoping.py", line 162, in do return getattr(self.registry(), name)(*args, **kwargs) File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2446, in flush self._flush(objects) File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2584, in _flush transaction.rollback(_capture_exception=True) File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 67, in __exit__ compat.reraise(exc_type, exc_value, exc_tb) File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2544, in _flush flush_context.execute() File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 416, in execute rec.execute(self) File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 583, in execute uow, File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 245, in save_obj insert, File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 1116, in _emit_insert_statements statement, params File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 980, in execute return meth(self, multiparams, params) File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 273, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1099, in _execute_clauseelement distilled_params, File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1174, in _execute_context e, util.text_type(statement), parameters, None, None File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1458, in _handle_dbapi_exception util.raise_from_cause(sqlalchemy_exception, exc_info) File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 296, in raise_from_cause reraise(type(exception), exception, tb=exc_tb, cause=cause) File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1171, in _execute_context context = constructor(dialect, self, conn, *args) File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 719, in _init_compiled for key in compiled_params File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 719, in <genexpr> for key in compiled_params File "/softs/bioinfo/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy/sql/type_api.py", line 1189, in process return impl_processor(process_param(value, dialect)) File "lib/galaxy/model/custom_types.py", line 319, in process_bind_param value = json_encoder.encode(value).encode() File "/softs/add-ons/Python-2.7.12/lib/python2.7/json/encoder.py", line 209, in encode chunks = list(chunks) File "/softs/add-ons/Python-2.7.12/lib/python2.7/json/encoder.py", line 434, in _iterencode for chunk in _iterencode_dict(o, _current_indent_level): File "/softs/add-ons/Python-2.7.12/lib/python2.7/json/encoder.py", line 408, in _iterencode_dict for chunk in chunks: File "/softs/add-ons/Python-2.7.12/lib/python2.7/json/encoder.py", line 387, in _iterencode_dict yield _encoder(key) StatementError: (exceptions.UnicodeDecodeError) 'utf8' codec can't decode byte 0xa5 in position 9: invalid start byte [SQL: u'INSERT INTO history_dataset_association_history (history_dataset_association_id, update_time, version, name, extension, metadata, extended_metadata_id) VALUES (%(history_dataset_association_id)s, %(update_time)s, %(version)s, %(name)s, %(extension)s, %(_metadata)s, %(extended_metadata_id)s) RETURNING history_dataset_association_history.id'] [parameters: [{'update_time': datetime.datetime(2019, 8, 26, 7, 53, 29, 457330), 'history_dataset_association_id': 3, 'extension': u'gff3.gz', 'extended_metadata_id': None, '_metadata': {'attribute_types': {'\xc4\xa5v\x10\x04>\xd5\x81U\xa5\\\xc7\xa2\xb3t_d\x07': 'str'}, 'comment_lines': 2528, u'dbkey': u'?', 'delimiter': '\t', 'columns': 9, 'column_types': ['str', 'str', 'str', 'int', 'int', 'float', 'str', 'str', 'str'], 'attributes': 1, 'data_lines': 38558}, 'version': 1, 'name': u'Final_ZmCML247v1a.collinearity.gff.gz'}]] Fred

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Gateways 2019 (San Diego): Register by Sept. 9 -- Keynote by James Taylor of Galaxy!
by Katherine Lawrence 22 Aug '19

22 Aug '19

* Gateways 2019 Monday through Wednesday, September 23-25, 2019Hosted at the Catamaran Resort in San Diego, CAhttps://sciencegateways.org/gateways2019 Science gateways allow science & engineering communities to access shared data, software, computing services, instruments, educational materials, and other resources specific to their disciplines. They are typically a web portal or a suite of desktop applications. Join gateway creators and enthusiasts to learn, share, connect, and shape the future of gateways. This year’s conference is co-located with eScience. Regular registration closes Monday, Sept. 9. (Book your hotel by Friday, August 23 for the best rates!) The conference program <https://sciencegateways.org/web/gateways2019/program>is already brimming with exciting keynotes, tutorials, and sessions, including James Taylor of Galaxy and author and science communication expert Randy Olson. The Poster Session is open to all.The deadline to submit a poster abstract has been extended to Tuesday, Sept. 3. <https://sciencegateways.org/web/gateways2019/program/cfp#poster> This conference is organized by the Science Gateways Community Institute (https://sciencegateways.org) Questions?Email help(a)sciencegateways.org. *

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King Skrupellos hack
by Pat Gillevet 21 Aug '19

21 Aug '19

Has anyone been hacked through the galaxy port 8080? We have an aberrant link on our install and I cannot find where it is hidden. The message that comes up is attached. Pat ******************************************************************************** Patrick M. Gillevet, Ph.D Director, Microbiome Analysis Center Professor, Department of Biology George Mason University, Science & Technology Campus 10900 University Boulevard, MSN 4D4 Manassas, Virginia 20110 Office 703-993-1057 Room Colgan Hall-426 FAX 703-993-8430 http://mbac.gmu.edu **********************************************************************************

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hudge size of _cleared_contents dir in job_working_directory
by Franck Giacomoni 21 Aug '19

21 Aug '19

Dear all, On a 19.1 galaxy version, my job_working_directory (database/ jobs_directory) contains a dir named _cleared_contents which continuously growing in terms of size… What is the exact process run by Galaxy to move a job from database/ jobs_directory/000/… to database/ jobs_directory/_cleared_contents Is there any configuration (in galaxy.yml) to manage this process? Can I delete this directory regularly or do I need to be careful of unfinished job already present in this specific dir (_cleared_contents)? Thank you very much for your reply Kindly regards Franck Franck Giacomoni Biological computing & Metabolomics franck.giacomoni(a)inra.fr<mailto:franck.giacomoni@inra.fr> UMR1019 - Human Nutrition Unit - Metabolism Exploration Platform Tél. : +33 (0)4 73 62 47 72 Fax : +33 (0)4 73 62 46 88 **Télétravail les mercredis 8h15-12h15 / 13h00-16h40** Centre de recherche de Clermont-Ferrand / Theix 63122 Saint Genès Champanelle France INRA PFEM portal<http://www6.clermont.inra.fr/plateforme_exploration_metabolisme> INRA Ingenum portal<https://www.ingenum.inra.fr/> MetaboHUB consortium website<http://www.metabohub.fr/metabohub.html> MetaboHUB Open Metabolic e-resources (OMeR)<https://informatique-mia.inra.fr/omer/> Workflow4Metabolomics.org portal<http://workflow4metabolomics.org/> PhytoHub Database website<http://phytohub.eu/> [/Users/fgiacomoni/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_2031791895]<https://workflow4metabolomics.org/w4e2020>

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August 2019 Galactic News: GCC2019 is done; BCC2020 is coming
by Dave Clements 01 Aug '19

01 Aug '19

Hello all, The August 2019 Galactic News is here! https://galaxyproject.org/news/2019-08-galaxy-update/ * Events: * GCC2019 is done (and yow, it was a success) * BCC2020 is coming to Toronto! * Galaxy ♥ BioHackathon Europe! * Plus deadlines this month and 19 other events in the next 90 days. * 178 new publications, including 5 highlighted ones. * Two new Galactic Blog posts: * Getting the most out of 1) Galaxy on Twitter, and 2) Pan-Galactic Search * Galaxy Platform News from UseGalaxy.* and the Human Cell Atlas. * Seven Open positions in four countries on two continents. * Updates to training materials and documentation. * New releases. This month's newsletter was a community effort unlike any before it. Thanks to everyone who contributed (and keep those contributions coming!). See you in San Diego, Milwaukee, Honolulu, Toronto, ... Dave C -- https://galaxyproject.org/

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Error when installing from toolshed
by Nancy Ide 31 Jul '19

31 Jul '19

Hello I am suddenly (after pulling a new version of galaxy) unable to install from the toolshed. The error is: Repository installation is not possible due to an invalid Galaxy URL: <b>None</b>. You may need to enable third-party cookies in your browser. Any idea how I can fix this? ----------------------------------------------------- Nancy Ide Professor of Computer Science Department of Computer Science Vassar College Poughkeepsie, New York 12604-0520 USA tel: (+1 845) 437 5988 fax: (+1 845) 437 7498 email: ide(a)cs.vassar.edu http://www.cs.vassar.edu/~ide -----------------------------------------------------

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Installing SOAPdenovo tools
by Peter Briggs 31 Jul '19

31 Jul '19

Dear Devs I was wondering if anyone on this list has experience of installing the SOAPdenovo tools from GigaGalaxy? The tool sources are hosted on github at https://github.com/gigascience/galaxy-bgisoap and the README says that the tools are hosted on the GigaToolshed at http://gigatoolshed.net/, but this doesn't seem to be accessible. I don't think manual installation from the github sources is practical. Does anyone have any suggestions or experience of installing these tools into their local Galaxy instances? Thanks! Best wishes Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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conda not installing deps.
by Jochen Bick 29 Jul '19

29 Jul '19

Hi we have a new galaxy 19.01 instance and conda is somehow not running correctly: galaxy.yml #dependency_resolvers_config_file: config/dependency_resolvers_conf.xml conda_prefix: /opt/galaxy/tools/_conda #conda_exec: null #conda_debug: false #conda_ensure_channels: 'iuc,conda-forge,bioconda,defaults' #conda_use_local: false conda_auto_install: true conda_auto_init: true conda_copy_dependencies: true job_working_directory: /opt/galaxy/daten/jobs_directory any ideas? Thanks Jochen -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 8092 Zurich, Switzerland Office: Eschikon 27 8315 Lindau, Switzerland Phone +41 52 354 92 06 jochen.bick(a)usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> www.ap.ethz.ch

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Memory limit for a Travis CI build
by Jin Li 28 Jul '19

28 Jul '19

Hi all, I submitted a PR to Galaxy Tools IUC (https://github.com/galaxyproject/tools-iuc/pull/2506) The Travis CI build exited with an error code 35072. The error may be caused by running out of memory. https://travis-ci.org/galaxyproject/tools-iuc/jobs/564531462 In fact, my program does not use too much memory on the test case (< 1GB). May I ask what is the memory limit to pass a Travis CI build? How could I request more memory if it is too small? Thank you. Best regards, Jin

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