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Galaxy Newsletter: July 2021
by Dave Clements 02 Jul '21

02 Jul '21

Hello all, The big news for July is that the 2021 Galaxy Community Conference <https://gcc2021.sched.com/> is under way. With GCC going on, this is one of our thinner newsletters <https://galaxyproject.org/news/2021-07-galaxy-update/>, but there are still *open positions <https://galaxyproject.org/news/2021-07-galaxy-update/#community-news>*, *event news <https://galaxyproject.org/news/2021-07-galaxy-update/#event-news>*, *Galaxy platform news <https://galaxyproject.org/news/2021-07-galaxy-update/#galaxy-platforms-news>*, *Galactic blog posts <https://galaxyproject.org/news/2021-07-galaxy-update/#galactic-blog-activity>*, *training and doc updates <https://galaxyproject.org/news/2021-07-galaxy-update/#doc-hub-and-training-…>*, recent *open-access Galaxy-related publications <https://galaxyproject.org/news/2021-07-galaxy-update/#publications>*, *new releases <https://galaxyproject.org/news/2021-07-galaxy-update/#releases>, and other news too <https://galaxyproject.org/news/2021-07-galaxy-update/#other-news>.* We hope to see you at GCC events this week and next. Dave Clements and Beatriz Serrano-Solano, Editors PS: It is too late to register for the 3 day conference next week. It is also officially too late to sign up for the CoFest on 9-10 July, but if you follow this link <https://docs.google.com/forms/d/e/1FAIpQLScdJHTzw7LWVxFaqGI30COZlcxGPksjGL_…>, you just mind find yourself invited anyway. -- https://gaaxyproject.org/ <https://galaxyproject.org/>

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Release of Galaxy 21.05
by Marius van den Beek 10 Jun '21

10 Jun '21

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 21.05. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/21.05_announce.html and user facing release notes are at https://docs.galaxyproject.org/en/master/releases/21.05_announce_user.html. A few release highlights are: ¡Galaxy, ahora en español! ------------------------------------ Thanks to Wendi Bacon, the Spanish language translation of Galaxy has been finalised and merged, so if you prefer to use Galaxy in Spanish, now you can! This update will be part of an ongoing project from Spanish speakers within the Galaxy community to keep the Galaxy interface localisation up to date, and to produce some Spanish language training materials in the GTN. Bugfixes and Stability ----------------------------- This release of Galaxy features fewer user-facing changes, as a huge amount of developer time went into making this a maintenance release with better testing, better stability, and more bugfixes. But watch out, this is all in preparation for the next release of Galaxy, 21.09, which will have some of the biggest changes in years! New development stack -------------------------------- Galaxy release 21.09 will ship with a new web framework (fastAPI <https://fastapi.tiangolo.com/>), Celery <https://docs.celeryproject.org/en/stable/index.html> task queue and process management using Circus <https://circus.readthedocs.io/en/latest/>. You can preview this new stack now by running *APP_WEBSERVER=dev ./run.sh*. Celery for background tasks -------------------------------------- Galaxy can now run certain tasks in the background. The Celery workers are currently not required, but if activated can perform certain long-running tasks, such as creating history export archives. Celery tasks will bridge the gap between rapid requests that can be handled during a web request and jobs that require extensive and relatively slow setup. More robust selection of job handlers ------------------------------------------------- Job throughput can be increased by starting Galaxy with multiple external job handler processes. Jobs were traditionally assigned to a job handler process by the web handler or workflow handler process that created the job. Since Release 19.01 Galaxy has supported additional mechanisms that use database serialization techniques to let job handlers assign processes to themselves. This mechanism is more robust and doesn't require that all job handler processes be alive and known by the web handler process. Galaxy now determines the best method for assigning jobs based on the database in use, if the assignment method is not set explicitly. Older job assignment methods will be removed in Galaxy release 21.09. For more details see the Job Handler Assignment Methods section <https://docs.galaxyproject.org/en/release_21.05/admin/scaling.html#job-hand…> of the Galaxy documentation. Check out the full release notes <https://docs.galaxyproject.org/en/master/releases/21.05_announce.html> for a lot more details, there are many more enhancements, new visualizations and bugfixes as well as instructions for upgrading your Galaxy installation. Thanks for using Galaxy!

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GCC2021 Deadlines Approaching
by Dave Clements 04 Jun '21

04 Jun '21

Hello all, The early registration deadline for the 2021 Galaxy Community Conference has been moved back to June 8. This gives you more time to take advantage of the 50% discount off full registration prices, so make sure you sign up now so you don't miss out! Register here <https://www.vibconferences.be/events/gcc2021-virtual-edition#attendees>. The draft program <https://gcc2021.sched.com/> and the speakers are now also available online. Please bear in mind that the times are set for the Europe/Middle East/Africa - Asia/Pacific window, and that the same schedule will run 9 hours later for the Americas. The availability of the speakers for the Q&A session will depend on the time zone in which they are located. Posters and demo sessions can still be submitted <https://www.vibconferences.be/events/gcc2021-virtual-edition#abstracts> until the 14th of June. Feel free to distribute this message further in your network. We hope to meet you online! Dave Clements on behalf of the GCC2021 Organizing Committee -- https://galaxyproject.org/

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June 2021 Galaxy Newsletter: All about GCC2021!
by Beatriz Serrano-Solano 31 May '21

31 May '21

Hello all, Welcome to the June 2021 edition of Galaxy News. GCC2021 is upon us, *with deadlines and events starting this month <https://galaxyproject.org/news/2021-06-galaxy-update/#featured-news>*. It's not too late to register (register by June 8 and get 50% off) and to submit Poster/Demo abstracts. Training week starts on June 28. We also started getting confirmations from speakers and are *publishing confirmed presenters <https://galaxyproject.org/news/2021-06-galaxy-update/#featured-news>* as we get them. We are also pleased to *announce our first three sponsors for GCC2021: F1000Research, GigaScience Press and KWS-SAAT <https://galaxyproject.org/news/2021-06-galaxy-update/#gcc2021-sponsorships>* . In addition to GCC news, we also released the *James Taylor birthday video <https://galaxyproject.org/news/2021-06-galaxy-update/#community-news>*, and have several *new open positions <https://galaxyproject.org/news/2021-06-galaxy-update/#community-news>*, lots of *event news <https://galaxyproject.org/news/2021-06-galaxy-update/#event-news>*, *Galaxy platform news <https://galaxyproject.org/news/2021-06-galaxy-update/#galaxy-platforms-news>*, *Galactic blog posts <https://galaxyproject.org/news/2021-06-galaxy-update/#galactic-blog-activity>*, *training and doc updates <https://galaxyproject.org/news/2021-06-galaxy-update/#doc-hub-and-training-…>*, recent *open-access Galaxy-related publications <https://galaxyproject.org/news/2021-06-galaxy-update/#publications>*, and *new releases <https://galaxyproject.org/news/2021-06-galaxy-update/#releases>.* As always, thanks for using Galaxy, Dave Clements and Beatriz Serrano-Solano, Editors PS: Subscribe to the Galaxy Announce mailing list <https://lists.galaxyproject.org/?count=100&all-lists=> to receive an email whenever this newsletter is published. -- Dr Beatriz Serrano-Solano (she/her) <https://www.hrc.org/resources/talking-about-pronouns-in-the-workplace> Bioinformatics Group Dept. Computer Science Albert-Ludwigs-Universität Freiburg Georges-Köhler-Allee, 106 70110 Freiburg Germany

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May 2021 Galaxy Newsletter: GCC2021 Deadlines Extended
by Dave Clements 04 May '21

04 May '21

Hello all, *The May 2021 edition of Galaxy News <https://galaxyproject.org/news/2021-05-galaxy-update/> is out! * The big news is that *several deadlines for the 2021 Galaxy Community Conference <https://galaxyproject.org/news/2021-05-galaxy-update/#community-news> have been extended, and the deadline for submitting James Taylor videos <https://galaxyproject.org/news/2021-05-galaxy-update/#featured-news> has been extended to this Friday.* And there are other upcoming deadlines too: - *ISMB/ECCB and BOSC 2021 abstracts <https://galaxyproject.org/news/2021-05-galaxy-update/#event-news> are due this Thursday.* - *Apply for the Galaxy Australia Variant Calling Workshops <https://galaxyproject.org/news/2021-05-galaxy-update/#event-news> by May 12.* We also have - *open positions <https://galaxyproject.org/news/2021-05-galaxy-update/#community-news>* - *webinars, CoFests, workshops, community meetups, and other events <https://galaxyproject.org/news/2021-05-galaxy-update/#event-news>*, - news about *public Galaxy platforms <https://galaxyproject.org/news/2021-05-galaxy-update/#galaxy-platforms-news>* , - recent *blog posts <https://galaxyproject.org/news/2021-05-galaxy-update/#galactic-blog-activity>* , - *training and doc updates <https://galaxyproject.org/news/2021-05-galaxy-update/#doc-hub-and-training-…>* , - recent *open-access Galaxy-related publications <https://galaxyproject.org/news/2021-05-galaxy-update/#publications>*, and - *new releases <https://galaxyproject.org/news/2021-05-galaxy-update/#releases>.* As always, thanks for using Galaxy, Dave Clements and Beatriz Serrano-Solano, Editors -- https://galaxyproject.org/

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April 2021 Galaxy newsletter
by Beatriz Serrano-Solano 13 Apr '21

13 Apr '21

Hello all, This newsletter coincides with the anniversary of James Taylor's death <https://galaxyproject.org/news/2021-04-galaxy-update/#featured-news> on April 2, 2020. James was a Galaxy Project founder and PI, and losing him at the same time as the global COVID-19 shutdown made for a tough month, and then a tough year for the Galaxy Community. To mark this, there are two items about James below. First, *a call to share your favorite story about James* via a 30 second video (by April 30). Second, there is a link to *a note to James* written by project leadership (mainly Anton). The other big news is that registration, abstract submission, and fellowship applications for the 2021 Galaxy Community Conference are now open <https://galaxyproject.org/news/2021-04-galaxy-update/#community-news>. Abstracts and fellowship applications are due by May 7. And as always there are sections on - *upcoming events <https://galaxyproject.org/news/2021-04-galaxy-update/#event-news>*, - news about *public Galaxy platforms <https://galaxyproject.org/news/2021-04-galaxy-update/#galaxy-platforms-news>* , - recent *blog posts <https://galaxyproject.org/news/2021-04-galaxy-update/#galactic-blog-activity>* , - *training and doc updates <https://galaxyproject.org/news/2021-04-galaxy-update/#doc-hub-and-training-…>* , - recent *open-access Galaxy-related publications <https://galaxyproject.org/news/2021-04-galaxy-update/#publications>*, and - *new releases <https://galaxyproject.org/news/2021-04-galaxy-update/#releases>.* It's been a memorable twelve months. It would have been easy to curl up and hide, but we kept going, addressed gaps, and helped address the global pandemic as well. Thanks for supporting each other, Dave Clements and Beatriz Serrano-Solano, Editors

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March 2021 Galaxy Newsletter
by Dave Clements 17 Mar '21

17 Mar '21

Hello all, It is a very busy time in the Galaxy. 2021 is young, but we have already had two large training events, including the largest Galaxy event ever - the GTN Smörgåsbord (with an amazing 1100+ people registered). We are ramping up for GCC2021, which will be online, global, and affordable, and will be more accessible (and likely much larger) than an in-person Galaxy Community Conference. Galaxy is also shifting with the times, and to reflect how our community has grown. This newsletter includes a new *Featured News <https://galaxyproject.org/news/2021-03-galaxy-update/#featured-news>* section highlighting 1) the *recent explosion of videos* related to Galaxy, 2) a draft *global governance model for Galaxy*, and 3) the new *Galaxy Career Center.* That's followed by another new section highlighting *community news <https://galaxyproject.org/news/2021-03-galaxy-update/#community-news>.* Arguably, *everything* here is community news, but items listed here particularly emphasize the community aspects of Galaxy. The newsletter still includes sections on - *upcoming events <https://galaxyproject.org/news/2021-03-galaxy-update/#event-news>*, - news about *public Galaxy platforms <https://galaxyproject.org/news/2021-03-galaxy-update/#galaxy-platforms-news>* , - recent *blog posts <https://galaxyproject.org/news/2021-03-galaxy-update/#galactic-blog-activity>* , - *training and doc updates <https://galaxyproject.org/news/2021-03-galaxy-update/#doc-hub-and-training-…>* , - recent *open-access Galaxy-related publications <https://galaxyproject.org/news/2021-03-galaxy-update/#publications>*, and - *new releases <https://galaxyproject.org/news/2021-03-galaxy-update/#releases>.* It's a lot to take in, but it all highlights the breadth and depth of the Galaxy Community. Enjoy, Dave Clements and Beatriz Serrano-Solano, Editors [image: 2021-03-16_14-51-56-wordcloud.png] -- https://galaxyproject.org/

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Release of Galaxy 21.01
by Marius van den Beek 16 Mar '21

16 Mar '21

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 21.01. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/21.01_announce.html and user facing release notes are at https://docs.galaxyproject.org/en/master/releases/21.01_announce_user.html. A few release highlights are: Workflows: Best Practices, Reports, Invocations ---------------------------------------------------------------- Workflows have seen huge improvements in this release! The workflow report editor is easier than ever to use, providing you with a list of common report components, interactive interfaces for embedding them in your reports, and a new workflow invocation tracker. You can now embed visualizations directly in your workflow reports making summarizing your analyses easier than ever. And, once your reports are produced, you can export them directly to pages to share your reports with colleagues.If you’re building advanced workflows utilizing Galaxy’s powerful sub-workflows for reusable workflow components, then you’ll be pleased to know you can now automatically update those to the latest version Remote Files ------------------ The Remote Files interface is an absolutely fantastic new way to browse your data. Inside Galaxy there is a new, abstract way to reference files locally and on other servers. This lets us provide a uniform interface to FTP servers, your Dropbox, public S3 buckets, and more! You'll find this under Choose Remote Files in the upload interface. This interface is also used for importing and exporting histories. Beta History Panel ------------------------- The History Panel is getting a refresh and a huge performance boost in the latest code. Does this sound exciting to you? Try it out now with the history menu option "Use Beta History Panel". This is not its final state but we'd love feedback from you, the users, on how you find it. It features both performance and usability improvements. E.g. now you can rename files without going into a separate menu, just double click the dataset title! Performance Improvements ------------------------------------- This release includes many performance improvements for browsing and searching Data libraries, improved job creation performance for certain classes of tools and copying Histories, Datasets and Dataset Collections Offload Zip Archive Creation to NGINX --------------------------------------------------- Galaxy can now utilize the NGINX module mod_zip to assemble and compress dataset collection and library dataset archives on the fly. This method is more efficient and can create large archives without affecting the Galaxy server process. The required setup is described in the admin documentation for proxying Galaxy with NGINX. Check out the full release notes <https://docs.galaxyproject.org/en/master/releases/21.01_announce.html> for a lot more details, there are many more enhancements, new visualizations and bug fixes as well as instructions for upgrading your Galaxy installation. Thanks for using Galaxy!

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February 2021 Galaxy Newsletter
by Beatriz Serrano-Solano 08 Feb '21

08 Feb '21

Hi Galaxy Community! The *February 2021 Newsletter <https://galaxyproject.org/news/2021-02-galaxy-update/#event-news>* is out. This time we announce that *GCC2021 goes virtual*, unfortunately. However, this will make it more affordable, and globally accessible to everyone. Other updates include: - *Event news <https://galaxyproject.org/news/2021-02-galaxy-update/#event-news>*: training, webinars, CoFests, conferences... - *Platform news <https://galaxyproject.org/news/2021-02-galaxy-update/#galaxy-platforms-news>*: ATACgraph, corGAT on Laniakea, UseGalaxy.eu - *9 Blog posts <https://galaxyproject.org/news/2021-02-galaxy-update/#galactic-blog-activity>* - *Training material and doc updates <https://galaxyproject.org/news/2021-02-galaxy-update/#doc-hub-and-training-…>*: Admin training, scRNA-seq, videos, new tutorials... - *Publications <https://galaxyproject.org/news/2021-02-galaxy-update/#publications>*: 8 highlights - *Who’s hiring?* <https://galaxyproject.org/news/2021-02-galaxy-update/#whos-hiring> more than 12 open positions - *New releases <https://galaxyproject.org/news/2021-02-galaxy-update/#releases>* - *Other news <https://galaxyproject.org/news/2021-02-galaxy-update/#other-news>* If you have anything to include to next month’s newsletter, then please send it to outreach(a)galaxyproject.org. Thanks for reading, Dave C and Bea

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January 2021 Galaxy Newsletter
by Dave Clements 07 Jan '21

07 Jan '21

Hello all, We are pleased to announce the first newsletter of 2021. As you can see there is a lot happening this month, starting with a working groups call about one hour from now. Thank you for persevering through 2020, and we hope that 2021 will be a better year for the world, and for this community. Dave Clements and Beatriz Serrano-Solano - *Event news <https://galaxyproject.org/news/2021-01-galaxy-update/#event-news>*: - 2nd Galaxy-ELIXIR webinar series, *starts January 20* - Galaxy Developer Roundtables, *January 7 & 21* - Papercuts CollaborationFest: *January 21* - Future Galaxy Admin Trainings, *Register your interest* - Tripal CodeFest 2021: *January 11-15* - Structural Variant Detection using ONT Data, *January 26* - GTN Smörgåsbord: A Global Galaxy Course. *Register by February 1* - Single-cell RNA-seq & network analysis using Galaxy and Cytoscape, *Apply by 26 February* - *Galaxy platform news <https://galaxyproject.org/news/2021-01-galaxy-update/#galaxy-platforms-news>:* - UseGalaxy.no - VINYL on Laniakea - W4M on UseGalaxy.fr - Center for Phage Technology server upgraded and improved - Plus more UseGalaxy.* news - *Blog posts <https://galaxyproject.org/news/2021-01-galaxy-update/#galactic-blog-activity>:* - Involvement of the Galaxy community in OLS-2 and invitation to apply to the next cohort - DDA and DIA proteomic analysis in Galaxy - GTN plant-related trainings - *Training material and doc updates <https://galaxyproject.org/news/2021-01-galaxy-update/#doc-hub-and-training-…>*: - Videos: Galactic Introductions - Videos: Quick Tips - *Publications <https://galaxyproject.org/news/2021-01-galaxy-update/#publications>* - Metaproteomics, CorGAT (SARS-CoV-2), GAIT-GM (metabolites), and training - *Q: Who's hiring? <https://galaxyproject.org/news/2021-01-galaxy-update/#whos-hiring>* - Europe: - Norwegian University of Life Science, IFB, VIB - North America: - Roche, Johns Hopkins (AnVIL, 2 positions; Galaxy, 2 Positions) - *New releases <https://galaxyproject.org/news/2021-01-galaxy-update/#releases>*: - Planemo 0.74.1 -- https://galaxyproject.org/

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