November 2021 - galaxy-dev - lists.galaxyproject.org

[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 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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