- galaxy-dev - lists.galaxyproject.org

Galaxy 24.2 Released
by Scott Cain 13 Feb '25

13 Feb '25

Dear Galaxy Community, We are thrilled to announce the release of Galaxy 24.2! This update brings a host of new features and enhancements designed to improve your workflow experience and boost productivity. Here are a few highlights: * A Wizard-like Export View for Workflow Invocations. * Workflow Editor Enhancements: Activity Bar and Undo Stack UI. * Masthead Revision and Activity Bar Improvements. * Improved Navigation and Usability of Collection Builders. * Enhanced Workflow Invocation View. * Display Metrics for Workflow Invocations. * Libraries Modernization: Directory Dataset Picker. * Live Reporting of Job Console Outputs. * ChatGXY - Job Error Wizard. For a detailed look at all the new features, please check out the User Release Notes< https://docs.galaxyproject.org/en/master/releases/24.2_announce_user.html>. We hope you enjoy the new features in Galaxy 24.1, and we look forward to your feedback! Thank you for using Galaxy! The Galaxy Team <https://galaxyproject.org/galaxy-team/> -- ------------------------------------------------------------------------ Scott Cain, Ph. D. Research Professor, Penn State Cite Us: * The Galaxy Community. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update, Nucleic Acids Research, 2024, https://doi.org/10.1093/nar/gkae410 How to cite specific Galaxy instances and tools: https://galaxyproject.org/citing-galaxy/

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GBCC 2025: The first-ever joint conference between Bioconductor and Galaxy!
by Natalie Whitaker-Allen 03 Sep '24

03 Sep '24

View this email in your browser<https://mailchi.mp/ff23e68393aa/join-the-galaxy-training-academy-2024-a-glo…> [https://mcusercontent.com/099b2f5f23bf0134dceb27c07/images/e7cd8365-a8b8-2f…]<https://galaxyproject.us22.list-manage.com/track/click?u=099b2f5f23bf0134dc…> [https://mcusercontent.com/099b2f5f23bf0134dceb27c07/images/7ec92f11-da39-99…] Hello Galaxy Community! We’re excited to announce that the Bioconductor and Galaxy communities are coming together for a Galaxy and Bioconductor Community Conference (GBCC 2025), our first joint conference, taking place from June 23-26, 2025, at Cold Spring Harbor Laboratory, New York. This unique event will bring together two of the leading platforms in genomic data science for a collaborative exploration of cutting-edge tools, methods, and research. GBCC 2025 will feature integrated sessions, workshops, and Birds of a Feather (BoF) discussions. By fostering collaboration across our communities, we aim to drive innovation and advance the field of bioinformatics. To celebrate we will launch a logo design contest for GBCC 2025! The winning design will become the official conference logo, featured on all conference materials, including stickers and t-shirts. More details on how to enter will be shared soon. Read more in our shared post on the Galaxy News and Bioconductor blog<https://galaxyproject.us22.list-manage.com/track/click?u=099b2f5f23bf0134dc…>, and stay tuned for further details about the conference. Mark your calendars for this milestone event in genomic data science! Thank you for being a part of Galaxy! Get more timely information by following us on Mastodon<https://galaxyproject.us22.list-manage.com/track/click?u=099b2f5f23bf0134dc…>, Bluesky<https://galaxyproject.us22.list-manage.com/track/click?u=099b2f5f23bf0134dc…>, and LinkedIn<https://galaxyproject.us22.list-manage.com/track/click?u=099b2f5f23bf0134dc…>! [https://mcusercontent.com/099b2f5f23bf0134dceb27c07/images/e7cd8365-a8b8-2f…]

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Galaxy 24.0 Release
by Natalie Whitaker-Allen 04 Apr '24

04 Apr '24

Hello Galaxy Community, We are thrilled to announce the release of Galaxy 24.0, packed with exciting new features and enhancements to improve your workflow experience. Here are some of the highlights: 1. New Workflow List and Card View: We've revamped the workflows user interface with new list and card views, along with quick access tabs for "My workflows," "Shared with me," and "Published workflows." 1. New ‘Select’ Component: A new component allows for selecting a large number of options with ease. It features a list-based layout, keyboard accessibility, and options for filtering and bulk selection. 1. Multiple Item Drag and Drop + Keyboard Navigation: You can now select multiple history items and drag them into other histories or tool forms. Keyboard navigation is also supported for easier history management. 1. Consolidated Resource Grids: Histories, visualizations, and pages are now consolidated into tab views for a more streamlined interface. 1. Move Datasets Between Storage Locations: Easily relocate datasets to new object stores using the new UI feature. The interface provides a clear visual representation of storage attributes and admin-provided details. To learn more about all that Galaxy 24.0 has to offer, please see the user release notes<https://docs.galaxyproject.org/en/master/releases/24.0_announce_user.html>. Upgrade today to take advantage of these enhancements and more! We are committed to continuously improving Galaxy to meet your needs and make your research more efficient. Your feedback is invaluable to us, so please don't hesitate to share your thoughts and suggestions. Thank you for using Galaxy! Bluesky<https://bsky.app/profile/galaxyproject.bsky.social> | Mastodon<https://mstdn.science/@galaxyproject> | LinkedIn<https://www.linkedin.com/company/galaxy-project>

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Announcing Galaxy 23.2: Exciting New Features and Enhancements!
by Natalie Whitaker-Allen 06 Feb '24

06 Feb '24

Hello, Galaxy Community! We are happy to announce the release of Galaxy 23.2, packed with exciting new features and enhancements to elevate your Galaxy skills and experience! Here are some the highlights of what's included in this release: * InvenioRDM Integration: We're excited to announce the integration of InvenioRDM into Galaxy! Import files directly from InvenioRDM repositories into Galaxy, and effortlessly publish Galaxy records, including Histories and datasets, to InvenioRDM. This integration streamlines data import and export processes, enhancing your overall Galaxy experience. * Introducing Workflow Comments: Collaborate like never before with our brand-new Workflow Comments feature in the Galaxy Workflow Editor. Now, you can visually explain and structure your workflows with ease, facilitating better communication and organization among team members. [Example of a structured workflow.] * Revamped Published Workflow Sharing Page: Experience a more informative, visually appealing, and user-friendly Published Workflow Sharing page. With new features such as a read-only mode, embedded interactive editor view, additional workflow information, and enhanced responsiveness for smaller screens, sharing and navigating workflows has never been smoother. [The new Workflow Sharing page.] Be sure to upgrade to Galaxy 23.2 to take advantage of these fantastic new features and upgrades! For detailed information on the full release, please refer to our user release notes<https://docs.galaxyproject.org/en/master/releases/23.2_announce_user.html>. We look forward to your continued support and feedback as we strive to continuously improve Galaxy! Thank you for being a part of Galaxy! Bluesky<https://bsky.app/profile/galaxyproject.bsky.social> | Mastodon<https://mstdn.science/@galaxyproject> | LinkedIn<https://www.linkedin.com/groups/4907635/>

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[GSoC 2023] Announcing Google Summer of Code 2023 - Open Genome Informatics organization application due 7th February
by Robin Haw 31 Jan '23

31 Jan '23

Dear All, Last week, Google announced this years’ Google Summer of Code (GSoC). GSoC is a global, online program focused on bringing new contributors into open source software development. GSoC contributors work with an open source organization on a 12+ week programming project under the guidance of mentors. The Open Genome Informatics team, which I administer with the help of Scott Cain and Marc Gillespie, serves as an “umbrella" organization to support the efforts of many open-access open-source bioinformatics projects for Google Summer of Code (GSoC<https://summerofcode.withgoogle.com/>). The list of previously involved projects includes JBrowse, Reactome, Galaxy, WormBase, and others. Over the last 12 years, we have been submitting applications to particiapte in GSoC. We are seeking project ideas to post and attract talented contributors to this years’ Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact me, Marc or Scott. You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2023>. For more information, please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC>. The program is open to students and to beginners in open source software development. The length of the projects is 175 and 350-hours, and there is an option to extend the program from the standard 12 weeks up to 22 weeks. Applications for organizations will close on February 7, 2023 at 18:00 UTC. So, if you are interested in taking part with the team, please let us know as soon as possible. Please forward this to others who might be interested in taking part. If you have any questions, please let us know. Thanks, Robin, Scott, and Marc Robin Haw, PhD Program Manager – Genome Informatics and Computational Biology Tel: 647-260-7985 robin.haw(a)oicr.on.ca<mailto:robin.haw@oicr.on.ca> Adaptive Oncology Ontario Institute for Cancer Research MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3 @OICR_news | oicr.on.ca<https://oicr.on.ca/> | genome informatics<https://oicr.on.ca/programs/genome-informatics/> | computational biology<https://oicr.on.ca/programs/computational-biology/> Collaborate. Translate. Change lives. This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

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European Galaxy Days, 3-7 Oct, Freiburg
by Beatriz Serrano-Solano 07 Sep '22

07 Sep '22

Dear all, We would like to invite you to the European Galaxy Days, which will take place in Freiburg (and online) from the 3rd to the 7th of October. The event will feature talks and demos with the latest updates from the community! Please find all the information in the event website: https://galaxyproject.org/events/2022-10-egd/ The registration for talks and demos closes on the 16th of September, registration for attendance to the event will be available until the 23rd of September. As soon as the registration for talks and demos is over, we will publish on the website a detailed program. Kind regards, Beatriz on behalf of the organizing team

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Release of Galaxy 22.05
by Marius van den Beek 23 Aug '22

23 Aug '22

Dear Community, We are pleased to announce the release of Galaxy 22.05. - Developer and admin release announcement <https://docs.galaxyproject.org/en/master/releases/22.05_announce.html>. - User release announcement <https://docs.galaxyproject.org/en/master/releases/22.05_announce_user.html> . A few release highlights are: The New History is Here After years of effort by the development team and community contributors, the new history is finally here. It's a big improvement over the old history interface, both technically and in terms of user experience, but it might take some getting used to. It has a lot of great new features like: - A quick switcher, letting you switch between recent histories - Easily find dataset inputs - Improved history search interface Check it out now! Storage Dashboard (Beta) Have you ever been over your quota? 250 GB sure goes fast! Now with the new Storage Dashboard you can get a quick overview of ways to help clean up deleted datasets and recover some of that quota allocation. This is a beta version of this interface, let us know if you have any issues. In future versions, it will be expanded to help you understand how your allocation is being used, and which histories and datasets should be cleaned up first. Bulk History Operations The new history allows for improved bulk operations, selecting dozens or hundreds of datasets to retag or change the database key automatically, a process that used to require using collections or doing them one by one. Deferred dataset resolution enables running workflows and tools without importing data into Galaxy first It is now possible to defer dataset resolution for datasets imported via URLs and the "Choose remote files" dialog. This means that the deferred dataset will only be downloaded as it is needed during job execution. Deferred datasets will not count towards your storage quota, as the data is not stored by Galaxy. To enable deferred dataset resolution click on "Settings" in the upload dialog. Workflow Improvements You can now see all invocations of a specific workflow, across all of your histories. This is especially useful if you run a single workflow across multiple datasets, and keep them nicely separated in multiple histories. You can see all of the results in a single centralised location. Additional workflow improvements have been made, e.g. numbering of steps in a workflow. Improvements have been made to the internal representation of the workflow that should make the saved .ga and .gxwf.yml files easier to compare across changes. Workflows can also now be zoomed in and out via scrolling, this interface should be more familiar for anyone who has used Google Maps: Saved Rules Do you use the Rule Based Uploader (RBU)? (If not, learn how today! <https://training.galaxyproject.org/training-material/topics/galaxy-interfac…>) The RBU now has a very convenient recently used rule listing, sorted by how recently they were used. You can hover over each entry to also list a preview of what steps were done in that RBU invocation. Scratchbook Upgraded The scratchbook has been updated to a new implementation. Now your views of datasets can overlap, you have much more freedom in the size of each window, and you can minimize datasets like minimizing a window to the taskbar in Windows. OpenAPI Docs The Galaxy API is going through an upgrade to FastAPI, which allows us to generate OpenAPI documentation <https://usegalaxy.org/api/docs>. If you're an API consumer, either via BioBlend or via another system, you can use this to see all of the APIs available from Galaxy and try them out live. Release Notes Please see the full release notes <https://docs.galaxyproject.org/en/master/releases/22.05_announce.html> for a lot more details and instructions for upgrading your Galaxy installation. Thanks for using Galaxy!

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Webinar Option Now Available for GCC2022
by Dave Clements 11 Jul '22

11 Jul '22

Hello all, This is a final reminder that registration is still open for GCC2022 and that you can now register for Webinar mode. See below for details. Hope to see you in Minneapolis in a week, Dave C *2022 Galaxy Community Conference (GCC2022)* July 17-23, 2022 University of Minnesota, Twin Cities Minneapolis, Minnesota, United States *#UseGalaxy2022 <https://twitter.com/hashtag/UseGalaxy2022>* *Unable to join us in Minneapolis for GCC2022? Registration now available for limited Webinar attendance!* Based on popular demand there is now a *Webinar mode* option for GCC2022 attendance. After registering for this option, you will get access to the live stream of the main meeting talks. You will also get invited to the conference Slack where you will have an opportunity to ask any questions of the presenters or poster authors. *Please note that in-person training events and CoFest will not be streamed. Also note that all speakers are required to attend in person. * Webinar Mode Registration Fee: $80 ($10 if working in a low-income country; see below) *If you are currently working in a low-income country <https://drive.google.com/file/d/1PW11lByYd61cIT7wPnGmTQpd9kM79EXX/view?usp=…>, as defined by the World Bank, please email Jenn Vessio <jvessio1(a)jhu.edu> before registering and ask for a discount code that you can apply during registration.* Register for GCC2022 Webinar Mode <https://galaxyproject.org/events/gcc2022/register> -- My last day with Galaxy was December 17, 2021 . After that I will be the Anaconda <https://www.anaconda.com/> open source community manager. If you need to reach Galaxy Outreach after December 17, please send your email to outreach(a)galaxyproject.org.

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Webinar Option Now Available for GCC2022
by Galaxy Community Conference 2022 08 Jul '22

08 Jul '22

GCC2022 July 17-23 ** 2022 Galaxy Community Conference (GCC2022) July 17-23, 2022 University of Minnesota, Twin Cities Minneapolis, Minnesota, United States #UseGalaxy2022 (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) ------------------------------------------------------------ Unable to join us in Minneapolis for GCC2022? Registration now available for limited Webinar attendance! Based on popular demand there is now a Webinar mode option for GCC2022 attendance. After registering for this option, you will get access to the live stream of the main meeting talks. You will also get invited to the conference Slack where you will have an opportunity to ask any questions of the presenters or poster authors. Please note that in-person training events and CoFest will not be streamed. Also note that all speakers are required to attend in person. Webinar Mode Registration Fee: $80 ($10 if working in a low-income country; see below) If you are currently working in a low-income country (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) , as defined by the World Bank, please email Jenn Vessio (mailto:jvessio1@jhu.edu) before registering and ask for a discount code that you can apply during registration. Register for GCC2022 Webinar Mode (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) ============================================================ ** Twitter (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) ** Website (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) Copyright © 2022 The Sapphyre Group, All rights reserved. You are receiving this email because you opted in via our website. Our mailing address is: The Sapphyre Group 7042 E Fish Lake Rd Maple Grove, MN 55311-2832 USA Want to change how you receive these emails? You can ** update your preferences (https://sapphyregroup.us14.list-manage.com/profile?u=0f49f912c8c0f3f17b049d…) or ** unsubscribe from this list (https://sapphyregroup.us14.list-manage.com/unsubscribe?u=0f49f912c8c0f3f17b…) . Email Marketing Powered by Mailchimp http://www.mailchimp.com/email-referral/?utm_source=freemium_newsletter&utm…

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Webinar mode for GCC2022 - Registration open
by Beatriz Serrano-Solano 27 Jun '22

27 Jun '22

Dear all, As you may know, the Galaxy Community Conference (GCC2022) will take place in Minnesota this year. For those that won't attend in person, the GCC Organizing Committee is happy to *announce a virtual webinar-like option*. How can you register? * There is a special *Virtual* option in the registration form <https://galaxyproject.org/events/gcc2022/register> for online only. * Once you are registered and a few days before the conference, you'll receive all the information you need, including: - an invitation to join the GCC2022 Slack space, - a link to a zoom webinar. Is it going to be interactive? There will be a Meeting Owl <https://owllabs.com/> on-site that will show you the room. In the webinar mode, you will have the chance to: * Watch the presentations live (remember the time difference!). * Ask questions. The chat and Q&A functionality will be enabled. There will be someone online in close contact with the moderator in the room. * If there's no time for more questions, you can always post them in the Slack channel. Will you be able to attend the poster session? Partially. The authors will deposit their posters in Sched <https://gcc2022.sched.com/>, and you'll have the chance to ask questions in Slack using the channel *gcc2022-posters-demo*. Their response may be slow, depending on how busy the poster presenters are in real life. How much will the virtual attendance cost? - Regular online registration: $80. - $10 for Low-Income-Countries (check this list <https://drive.google.com/file/d/1PW11lByYd61cIT7wPnGmTQpd9kM79EXX/view> to find out which countries qualify as such). When is the deadline for registration? - July 15. Thank you all for all the interest that you've been showing to join GCC2022, regardless of the format. That's great to see! Cheers, Beatriz on behalf of the GCC2022 Organizing Committee

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