galaxy-dev February 2020

galaxy-dev@lists.galaxyproject.org

5 participants
6 discussions

Error keeps occuring
by Hill-Spanik, Kristina M 28 Feb '20

28 Feb '20

Hi, I keep getting the following error. Any help would be appreciated. Thanks, Kristy ________________________ Kristina Hill-Spanik Lab Manager Molecular Biology Core Facility Grice Marine Lab College of Charleston 205 Fort Johnson Road Charleston, SC 29412 hillkm1(a)cofc.edu<mailto:hillkm1@cofc.edu> 843-953-9193 An error occurred while updating information with the server. Please contact a Galaxy administrator if the problem persists. { "userAgent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_6) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/13.0.5 Safari/605.1.15", "onLine": true, "version": "20.01", "xhr": { "readyState": 4, "responseText": "{\"err_msg\": \"Uncaught exception in exposed API method:\", \"err_code\": 0}", "responseJSON": { "err_msg": "Uncaught exception in exposed API method:", "err_code": 0 }, "status": 500, "statusText": "Internal Server Error" }, "options": { "validate": true, "parse": true, "method": "delete", "emulateHTTP": false, "emulateJSON": false, "textStatus": "error", "errorThrown": "Internal Server Error" }, "url": "https://usegalaxy.org/history/view_multipl/api/histories/a07a6d267500b6b2/c…", "data": { "collection_type": "list:paired", "deleted": true, "history_content_type": "dataset_collection", "model_class": "HistoryDatasetCollectionAssociation", "populated_state_message": null, "job_source_id": "80374338f06ac04b", "history_id": "a07a6d267500b6b2", "type": "collection", "job_source_type": "ImplicitCollectionJobs", "hid": 3371, "type_id": "dataset_collection-e6d871d8a2cf90c0", "tags": [], "update_time": "2020-02-26T14:05:47.592Z", "name": "FastQC on collection 3370: Webpage", "visible": true, "url": "/api/histories/a07a6d267500b6b2/contents/dataset_collections/e6d871d8a2cf90c0", "populated_state": "new", "id": "e6d871d8a2cf90c0", "create_time": "2020-02-26T14:05:47.592Z", "element_count": 153, "recursive": true, "purge": true, "elements": [] }, "model": { "collection_type": "list:paired", "deleted": true, "history_content_type": "dataset_collection", "model_class": "HistoryDatasetCollectionAssociation", "populated_state_message": null, "job_source_id": "80374338f06ac04b", "history_id": "a07a6d267500b6b2", "type": "collection", "job_source_type": "ImplicitCollectionJobs", "hid": 3371, "type_id": "dataset_collection-e6d871d8a2cf90c0", "tags": [], "update_time": "2020-02-26T14:05:47.592Z", "name": "FastQC on collection 3370: Webpage", "visible": true, "url": "/api/histories/a07a6d267500b6b2/contents/dataset_collections/e6d871d8a2cf90c0", "populated_state": "new", "id": "e6d871d8a2cf90c0", "create_time": "2020-02-26T14:05:47.592Z", "element_count": 153, "recursive": true, "purge": true, "elements": [] }, "user": { "id": "962c63e5584bc3ea", "username": "khillspanik", "total_disk_usage": 49650284207, "nice_total_disk_usage": "46.2 GB", "quota_percent": 18, "is_admin": false, "preferences": {}, "model_class": "User", "deleted": false, "active": true, "last_password_change": "2019-12-05T14:12:35.446534", "tags_used": [] } }

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Release of Galaxy 20.01
by Marius van den Beek 27 Feb '20

27 Feb '20

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 20.01. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/20.01_announce.html and user facing release notes are at https://docs.galaxyproject.org/en/master/releases/20.01_announce_user.html. A few release highlights are: Workflow Executions Menu ------------------------ This menu can be reached from the User menu -> Workflow Invocations and lists your recent Workflow executions, their status and links to the Workflow Editor and the History with the results of the Workflow run. Enhanced workflow functionality ------------------------------- Workflows can now make use of optional datasets and optional parameters, optional parameter default values and dataset inputs can now be restricted to user-defined datatypes. The workflow editor and execution engine have been enhanced to allow defining options to choose from, and these options can be connected to compatible text, integer, float, color and select tool parameters for more flexible and universally reusable workflows Galay Markdown Pages and Workflow Reports as PDF ------------------------------------------------ An additional link has been added to Galaxy Markdown Pages and Workflow reports that exports your document as a standalone PDF. Screen Reader friendly Navigation -------------------------------- The top menu and the Workflow Editor have been improved for easier navigation using Screen Readers and the Keyboard. Email-notification for completed jobs ------------------------------------- You can now select to be notified by email when a tool run has finished. Check out the release notes for a lot more details - there are many more enhancements such as new interface elements, visualizations, datatypes and bug fixes as well as instructions for upgrading your Galaxy installation to Python 3. Thanks for using Galaxy!

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issues file uploading
by Thomas BOUTET 27 Feb '20

27 Feb '20

Hello, I have issues uplaoding .bed data on galaxeast. I am sure the data and format is fine as I am able to upload the same file in Galaxy. Yesterday I uploaded several .bed files and everything works fine. As I didn’t reach my quota (90GB) I am sure this is not the problem. Thank you very much for your help.

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Fwd: [GMOD-devel] GMOD in Google Summer of Code
by Dave Clements 21 Feb '20

21 Feb '20

Hi All, Scott's "But WAIT!" comment applies to Galaxy too. :-) See below if you have an idea. Cheers, Dave C ---------- Forwarded message --------- From: Scott Cain <scott(a)scottcain.net> Date: Thu, Feb 20, 2020 at 6:16 PM Subject: [GMOD-devel] GMOD in Google Summer of Code To: gmod-announce <gmod-announce(a)lists.sourceforge.net>, gmod-ajax < gmod-ajax(a)lists.sourceforge.net>, gmod tripal devel < gmod-tripal-devel(a)lists.sourceforge.net>, Gbrowse (E-mail) < gmod-gbrowse(a)lists.sourceforge.net>, GMOD Schema/Chado List < gmod-schema(a)lists.sourceforge.net>, gmod-devel < gmod-devel(a)lists.sourceforge.net>, <apollo(a)lbl.gov>, maker-devel(a)yandell-lab.org List <maker-devel(a)yandell-lab.org> Hello, I am very pleased to announce that GMOD in conjunction with Reactome, Galaxy and OICR/WormBase, together forming Open Genome Informatics, has been accepted for the Google Summer of Code. If you or someone you know might be a student interested in participating in GSoC, please take a look at http://gmod.org/wiki/GSOC_Project_Ideas_2020 where there are proposed projects that cover a fair number of technologies. Official proposals from students will be due in mid March (more on that later). But WAIT! There's more: if you might be interested in being a mentor and working with a student this summer, it's not too late! You can add new project ideas to the page above (contact me if you need an account), or you can even volunteer to add yourself to one of the existing ideas as a potential mentor. Please feel free to forward this to other mailing lists or people who might be interested. We are already an eclectic, dispersed group, so everyone is welcome. Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research _______________________________________________ Gmod-devel mailing list Gmod-devel(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/gmod-devel -- https://galaxyproject.org/

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Installing from toolshed
by Omar Ali 11 Feb '20

11 Feb '20

I am trying to install the denovo RNA seq tools to galaxy from the toolshed ( https://toolshed.g2.bx.psu.edu/ ) but it is not allowing me to. can you assist please. -- Regards, Omar Ali. B.Sc. Biology & Environmental and Natural Resource Management (2012-2015) M.Phil. Microbiology (2015-2018) Ph.D. Microbiology Candidate (2018- present) U.W.I. #Remember to always help those in need. #Always be brave and have courage

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BCC2020 Training Topic Voting is Open
by Dave Clements 11 Feb '20

11 Feb '20

Hello all, The The Bioinformatics Community Conference (BCC2020) <https://bcc2020.github.io/>, will bring together the Galaxy Community Conference (GCC) and the Bioinformatics Open Source Conference (BOSC) in Toronto, Canada in July 2020, following ISMB 2020 <https://www.iscb.org/ismb2020> in Montréal. BCC2020 will start with a dedicated training day, followed by 3 days of mixed meeting and training events. The community (you!) determines what training will be offered at BCC2020. *Nominations from the community <https://bcc2020.github.io/training/>* are now ready for review and voting. If you are possibly attending BCC2020 then please take a few minutes to review the nominations and then submit your ballot <https://docs.google.com/forms/d/e/1FAIpQLSfmOowsHt0cL1ukiGvOdh7WxWKoSuT-3GM…>. Voting closes on February 21. Thanks in advance for your input, and we hope to see you in Toronto, BCC2020 Organizers -- https://galaxyproject.org/

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galaxy-dev February 2020