August 2019 - galaxy-dev - lists.galaxyproject.org

Gateways 2019 (San Diego): Register by Sept. 9 -- Keynote by James Taylor of Galaxy!

by Katherine Lawrence

* 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

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 **********************************************************************************

2 days, 4 hours

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hudge size of _cleared_contents dir in job_working_directory

by Franck Giacomoni

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>

2 days, 13 hours

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set up an asynchronous data source in galaxy

by SAPET, Frederic

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... 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

3 days, 13 hours

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August 2019 Galactic News: GCC2019 is done; BCC2020 is coming

by Dave Clements

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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galaxy-dev August 2019