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GCC2022 Highlights and Updated Deadlines
by Galaxy Community Conference 2022 17 Jun '22

17 Jun '22

July 17-23 | Minneapolis, MN ** 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…) ------------------------------------------------------------ Three years of waiting and we're down to one month before the #usegalaxy (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) community meets in person at GCC2022! View a summary here (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) of what to expect when you join us in Minneapolis. Not Registered Yet? There's Still Time! Registration has been EXTENDED to Wednesday, June 22 - register here for GCC2022 (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) ! Meeting Registration Fees Full (< June 22) Late (> June 23) Student/postdoc $400 $500 Academic / Non-Profit / Government $550 $750 Industry $900 $1,150 Michael Schatz at GCC2022 What do TIME100 (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) and GCC2022 have in common? Michael Schatz, that's what! Come talk to him about the future, learn more about his Birds of a Feather session here (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) . We have a tremendous lineup of speakers for our accepted and invited talks and training sessions! Get to know who they are by viewing the entire GCC2022 schedule (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) . Hotel Reservation Deadline EXTENDED Be sure to make your hotel reservations (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) at our GCC2022 venue the Courtyard Minneapolis Downtown by Thursday, June 30 to get our conference rate of $139/night! Register for GCC2022 by June 22 (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) Make Hotel Reservations by June 30 (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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[GSoC2021] [OGI] Participation in Google Summer of Code 2021
by Robin Haw 15 Mar '22

15 Mar '22

Dear All, The Open Genome Informatics team serves as an “umbrella" organization to support the efforts of many open-access open-source bioinformatics projects for <https://summerofcode.withgoogle.com/> Google Summer of Code (GSoC<https://summerofcode.withgoogle.com/>). Among this list of projects are Reactome and GMOD and its software projects -- JBrowse; Galaxy; WormBase; and others. Call for 2021 Project Ideas and Mentors: We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2021>. For more information please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC><http://gmod.org/wiki/GSoC#Google_Summer_of_Code_2020>. The mentoring organization application deadline with GSoC is February 19th at 2 pm EST. 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, Marc, and Scott.

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Release of Galaxy 22.01
by Marius van den Beek 15 Mar '22

15 Mar '22

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 22.01. - Developer and admin release announcement <https://docs.galaxyproject.org/en/master/releases/22.01_announce.html>. - User release announcement <https://docs.galaxyproject.org/en/master/releases/22.01_announce_user.html> . A few release highlights are: New Colour Selector Do you use tools which require colour inputs, like Circos? Previously, we had a very restricted colour input which gave you a very limited palette. Now, you have complete freedom of choice with the modern colour selector. Improved File Export If you've been exporting files from Galaxy lately, you've probably seen the amazing new remote file source export, which allows you to export files to FTP, Dropbox, and other locations. Improved File Uploads Previously, Galaxy servers used a variety of methods to let you upload large files easily, including some servers which required FTP for large files. We have replaced this with a new upload method, which will be enabled on all usegalaxy servers soon. This will make file uploads significantly smoother, and will be more tolerant of network failures and interruptions! You do not need to make any changes. Beta History: Collection Improvements If you've been trying out the beta history (which will be the default history in the next release!), it has been updated to indicate whether collections are homogeneous or heterogeneous. This will help you see more easily if you've accidentally included an incorrect dataset. Galaxy starts as a FastAPI application by default Starting Galaxy via run.sh will use the new gravity process manager <https://github.com/galaxyproject/gravity>. The new configuration uses Gunicorn <https://gunicorn.org/> and FastAPI <https://fastapi.tiangolo.com/> to drive Galaxy's web process, and starts job handler and Celery <https://docs.celeryproject.org/> processes automatically. For more details and instructions, please consult the Migrating to Gunicorn documentation <https://docs.galaxyproject.org/en/latest/admin/migrating_to_gunicorn>. User Preferences can be encrypted in Galaxy Vault Galaxy can now be configured to store secrets in an external vault, which is useful for secure handling and centralization of secrets management. In particular, information fields in the "Manage information" section of the user profile, such as dropbox keys, can be configured to be encrypted at rest in a vault (Hashicorp, Custos or database) instead of being stored as plain text in the user preferences table. For detailed information on configuration, refer to the vault section <https://docs.galaxyproject.org/en/release_22.01/admin/special_topics/vault.…> of the admin documentation. Release Notes Please see the full release notes <https://docs.galaxyproject.org/en/latest/releases/22.01_announce.html> for a lot more details and instructions for upgrading your Galaxy installation. Thanks for using Galaxy!

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2022 Galaxy Community Conference (GCC2022): July 17-23 in Minneapolis, MN, USA
by Enis Afgan 28 Feb '22

28 Feb '22

2022 Galaxy Community Conference (GCC2022) July 17-23, Minneapolis, Minnesota, USA https://galaxyproject.org/events/gcc2022/ Deadlines: April 12: Oral presentation and lightning talk abstracts due <https://docs.google.com/forms/d/1z29z8Nd8Gho0trS7DySvWAii6hisbZr67cuI--lcZ_…> May 12: Early registration <https://learning.umn.edu/portal/events/reg/participantTypeSelection.do?meth…> ends June 3: Demo and poster abstracts due <https://docs.google.com/forms/d/1z29z8Nd8Gho0trS7DySvWAii6hisbZr67cuI--lcZ_…> The 2022 Galaxy Community Conference (GCC2022) <https://galaxyproject.org/events/gcc2022/> will be held July 17-23 in Minneapolis, Minnesota. GCC brings together hundreds of faculty, clinicians, researchers, and students, all working in and supporting data intensive science that is accessible, shareable, and reproducible. GCC2022 features oral presentations, lightning talks, posters, demos, birds-of-a-feather gatherings (BoFs), training, a CollaborationFest, and plenty of opportunities for networking. Presentations will cover the full spectrum of Galaxy applications, enhancements, and deployments. If you are working in data intensive science then GCC2022 is an ideal conference for sharing your work, learning from others, and finding new collaborators. Present your work! Abstract submission <https://docs.google.com/forms/d/1z29z8Nd8Gho0trS7DySvWAii6hisbZr67cuI--lcZ_…> for talks, lightning talks, demos, and posters is now open. If you work in data-intensive science then please consider presenting your work at GCC2022. This is a chance to present to 200+ researchers, all addressing challenges in data intensive science. Abstract submissions for oral presentations are due on April 12. Submit an abstract (or two) now! <https://docs.google.com/forms/d/1z29z8Nd8Gho0trS7DySvWAii6hisbZr67cuI--lcZ_…> Topics of Interest If you’re currently working on any of these topics, this conference is for you: - Omics data analysis: genomic sequencing, microbiome, proteomics, imaging, you name it! - Tools and visualizations for working with omics data - Compute infrastructure for enabling data intensive science - Galaxy applications in any domain or topic: ML, climate, NPL, … - Outreach and training related to data analysis Registration Registration information is available on the conference website <https://galaxyproject.org/events/gcc2022/register#in-person>. Early registration ends May 12. So, register <https://galaxyproject.org/events/gcc2022/register> early! About Galaxy Galaxy <https://galaxyproject.org/> is a platform for data integration and analysis in the life sciences. It enables researchers to build, run, share, and repeat their own complex computational analyses using only a web browser and without having to first learn system administration and command line interfaces. The Galaxy Project is driven by a vibrant community who publish workflows and analyses, wrap new tools, maintain and enhance the source code, provide support, and write documentation and training materials. Galaxy is open-source and freely available, and is deployed in hundreds of organizations, running on everything from laptops to supercomputers to public and private clouds. Over 150 of these platforms are publicly available and can be used with little or no setup. Thousands of tools have been ported to Galaxy and are deployable from the Galaxy Tool Shed. Galaxy was developed to support life science research, but the platform is domain agnostic and is now used in domains as diverse as natural language processing, computational solid geometry, and social science. Hope to see you in Minneapolis! GCC2022 Organizers <https://galaxyproject.org/events/gcc2022/organizers/>

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Galaxy community paper
by Björn Grüning 30 Jan '22

30 Jan '22

Hi all, we have been accepted to publish an updated version of the Galaxy community paper 🎉 If you’ve made substantial contributions to the Galaxy community ecosystem (core framework, tools, GTN, public server maintenance, user support, etc.) over the past two years, please add your details as an author into this form: https://bit.ly/nar-author-2022 Thank you all! Bjoern

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Cannot update tool on toolshed
by petr＠umbr.cas.cz 24 Jan '22

24 Jan '22

I have repository https://toolshed.g2.bx.psu.edu/repository/browse_repository?id=691d87250e82… When I try to update repository by uploading either tarball or single file, nothing happen - I got a blank page which never updates. When I explored the content of this repository it look like the content was updated partially - Toolshed still shows the revision number 0 but content of files visible through toolshed is updated. However, linked mercurial repository at https://petr-novak@toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotatio… does not have this update. So the content visible through tooshed interface different from content of hg repository. This is not a first time it happened, I have also other repositories which cannot be updated. Is it a bug or am I doing something wrong? Petr

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10 years of the Galactic News: we need your help
by Beatriz Serrano-Solano 10 Jan '22

10 Jan '22

Dear all, Happy new year! For 10 years, we have been sharing news through the monthly Galactic News. This is a milestone and we are so proud of the community that we built together. A lot can change over 10 years and we want to know which parts of the Galaxy newsletter are the most useful and which parts may need to be modified to suit your needs. Please take *2 minutes to fill out **this survey <https://docs.google.com/forms/d/e/1FAIpQLSdws7R3y_4qB4LNNbqx4qYRNlkmuwmnqQ5…>* so that we can create a newsletter that will better serve our growing community. Thank you for reading and here's to the next 10 years, Assunta and Bea

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Release of Galaxy 21.09
by Marius van den Beek 02 Nov '21

02 Nov '21

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 21.09. - Developer and admin release announcement <https://docs.galaxyproject.org/en/latest/releases/21.09_announce.html> - User release announcement <https://docs.galaxyproject.org/en/latest/releases/21.09_announce_user.html> . A few release highlights are: Tool Panel Views We now have "Tool Panel Views"! These are different views into the same toolbox and might help make it easier to find the tools you want. In the future, there are plans to create user-customisable toolboxes, but until then go explore the new EDAM Ontology-based toolboxes which organise tools around scientific areas or processes. For example, a category like "Filtering" might have tools like "select lines" or "filter bam by quality", both doing the same process of filtering, despite their different file types and formats. Unfortunately, not all tools are fully annotated yet, and while we also pull terms from bio.tools, this still doesn't get us full coverage and many tools will still appear under a large section "Uncategorized". Hopefully, this will improve as users and tool developers annotate these tools with the appropriate terms that help everyone find them. Collections (Beta History Updates) Did you ever create *a collection with the wrong dbkey or datatype*? Well, in the Beta History you can now change collections' datatypes and dbkeys! This should save a lot of time for everyone working with large datasets (Pull Request 11799 <https://github.com/galaxyproject/galaxy/pull/11799/>). Additionally, did a *collection ever fail* for you? And you wondered why? Now you can find out with the view details button for collections (Pull Request 12261 <https://github.com/galaxyproject/galaxy/pull/12261>)! Importing Data Selecting datasets from the Remote Files view has gotten easier! Now, you can select folders and files and import at once all of the datasets recursively in those folders. Previously, you could only select files within a folder, so this is a huge improvement in the usability of such a key new feature of Galaxy (Pull Request 12310 <https://github.com/galaxyproject/galaxy/pull/12310>). But with great power comes great responsibility, be careful not to import the entirety of NCBI! Reports Report components used to automatically arrange themselves in a smart way, but due to some issues with the floating of components, these will now be full width until we can figure out a good way to provide a similar feature (Pull Request 12085 <https://github.com/galaxyproject/galaxy/pull/12085>). Enhancements for Working with Remote Data and Distributed Computing Resources Many fixes and enhancements were made to improve how Galaxy can import and write to remote data using the configured file source plugins. In addition to the History Export functionality, which can write to remote locations, we have added an Export datasets Tool for exporting individual Datasets and Dataset collections to configured remote locations. The Tool will automatically maintain the name and structure of Datasets and Dataset Collections. We have added the possibility to import entire folders of remote data and made the data selection dialog more intuitive. We also added numerous improvements and fixes to the extended metadata collection strategy and Pulsar <https://github.com/galaxyproject/pulsar>, so that many more tools are able to run in Pulsar <https://github.com/galaxyproject/pulsar> and write data back to storage without passing through Galaxy first. Migration to FastAPI and Extended Documentation of API Routes We have modernized and migrated many more API routes to FastAPI and have extended the documentation and validation of these routes. Migration to SQLAlchemy 1.4 and Declarative Mapping Galaxy is now using SQLAlchemy <https://www.sqlalchemy.org/> version 1.4, which is a prerequisite for asynchronously interacting with the database. We also modernized the way our database models are defined to the more commonly used Declarative Mapping approach, which is more concise and better documented. Modernization of Tool Form Interface The tool form interface has been almost completely migrated from Backbone <https://backbonejs.org/> to Vue <https://vuejs.org/>. This improves the reactivity of parameter validation and enables the migration of tool parameters to Vue, which will also allow us to add many more types of tool parameters. We further migrated the tool form variant for the Workflow Editor, the Workflow run form and the Show Dataset Parameter page to Vue. New User Welcome Page We have added a page that new users will be directed to after creating a new Galaxy account. Release Notes Please see the full release notes <https://docs.galaxyproject.org/en/latest/releases/21.09_announce.html> for a lot more details and instructions for upgrading your Galaxy installation. Thanks for using Galaxy!

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November 2021 Galaxy Newsletter
by Dave Clements 01 Nov '21

01 Nov '21

Happy November from Galaxy! The November newsletter is thin, *but powerful*: - Galaxy India Launches this Month <https://galaxyproject.org/news/2021-11-galaxy-update/#community-news> - 7 new openings (13 total) <https://galaxyproject.org/news/2021-11-galaxy-update/#community-news> - 9 upcoming Events <https://galaxyproject.org/news/2021-11-galaxy-update/#event-news> - Blog posts on SARS-CoV-2 training in Africa; Sunsetting CloudLaundh; and TIaaS <https://galaxyproject.org/news/2021-11-galaxy-update/#galactic-blog-posts> - UseGalaxy.* Updates <https://galaxyproject.org/news/2021-11-galaxy-update/#galaxy-platforms-news> - Other News too: BY-COVID Launches <https://galaxyproject.org/news/2021-11-galaxy-update/#other-news> Have something for the next newsletter? Please let us know and we will spread the word. Beatriz Serrano-Solano and Dave Clements, Editors -- https://galaxyproject.org/

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October Galaxy News
by Dave Clements 11 Oct '21

11 Oct '21

Hello all, The October Newsletter is out <https://galaxyproject.org/news/2021-10-galaxy-update/>. and it covers Galaxy involvement in Hacktoberfest, and Outreachy, plus a nice batch of trainings, talks and a Galaxy Papercuts CoFest day too. It also brings news of new job openings on two continents, two new platforms, blog posts (where My Little Pony makes an appearance, really), GTN updates (few in number but big in their coolness), publications, and releases. In other words, another active month in the Galaxy. Beatriz Serrano-Solano and Dave Clements, Editors -- https://galaxyproject.org/

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