- galaxy-announce - lists.galaxyproject.org

Galaxy Release 19.01
by Dave Clements 28 Feb '19

28 Feb '19

We are pleased to announce the *release of Galaxy 19.01 <https://docs.galaxyproject.org/en/release_19.01/releases/19.01_announce.html>*. A few release highlights are: <https://galaxyproject.org/news/2019-1-galaxy-release/#revised-ui-style> Revised UI Style The Galaxy stylesheet has been substantially reworked resulting in the largest visual refresh to Galaxy in years. <https://galaxyproject.org/news/2019-1-galaxy-release/#more-colorful-tags> More Colorful Tags Use consistently hashed randomized colors for history dataset name tags to increase visual distinction between tags, making it easier to track data flow in complex histories. Thanks to @erasche <https://github.com/erasche>. <https://galaxyproject.org/news/2019-1-galaxy-release/#extensive-workflow-en…> Extensive Workflow Enhancements (continued) Galaxy 18.09 featured a bunch of important and diverse fixes and enhancements to workflows on both the frontend and backend. That progress continues in release 19.01. The workflow editor now features explicit step parameter nodes for non-file data (integers, strings, booleans, etc) and the ability to connect these to all tool inputs - not just files. The YAML-based Galaxy Format 2 workflow language is now included in Galaxy as a beta option and allows import and export of human readable workflows as well as extensions to allow Galaxy to serve as a file editor for such workflows. The workflow editor features more helpful labels on inputs and outputs and important fixes including logic for connecting collections and dealing with missing tools. The workflow run form now deals with default values more correctly. <https://galaxyproject.org/news/2019-1-galaxy-release/#enhanced-support-for-…> Enhanced Support for Singularity Singularity <https://singularity.lbl.gov/> container support in Galaxy has been brought to parity with Docker container support. Specifically, Galaxy can now be configured to fetch Biocontainers <https://biocontainers.pro/> automatically for enabled job destinations. Moreover, explicitly annotated Docker containers (either in tools or job destinations) can be used with Singularity. Thanks to @mvdbeek <https://github.com/mvdbeek> Please see the full release notes <https://docs.galaxyproject.org/en/release_19.01/releases/19.01_announce.html> for more information, including how to upgrade today! *Thanks for using Galaxy!* -- https://galaxyproject.org/ https://usegalaxy.org/

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February 2019 Galaxy News: VOTE RIGHT NOW, and other stuff too.
by Dave Clements 01 Feb '19

01 Feb '19

Hello all, The *February 2019 Galactic News* <https://galaxyproject.org/news/2019-02-galaxy-update/> is here! - Event News <https://galaxyproject.org/news/2019-02-galaxy-update/#event-news> - *Voting on GCC2019 training topics open through February 4th! <https://galaxyproject.org/news/2019-02-galaxy-update/#gcc2019-training-topi…>* . - *ELIXIR Galaxy Community Workshop <https://galaxyproject.org/news/2019-02-galaxy-update/#elixir-galaxy-communi…>* pre-registration is open! - GalaxyAdmins needs your topic suggestions <https://galaxyproject.org/news/2019-02-galaxy-update/#galaxyadmins-needs-yo…> . - 160 new publications <https://galaxyproject.org/news/2019-02-galaxy-update/#publications>, great resources lead to great insight. - Some most excellent Galaxy Platform News <https://galaxyproject.org/news/2019-02-galaxy-update/#galaxy-platforms-news>, including proteo-transcriptomics, RNA analyis tools, Genome Browsers, and more! - The Tutorial of the Month is ... Genome annotation with Prokka <https://galaxyproject.org/news/2019-02-galaxy-update/#new-galactic-blog-pos…> ! - At least 23 Open positions <https://galaxyproject.org/news/2019-02-galaxy-update/#whos-hiring> in 6 countries on 2 continents. - Doc, Hub, and Training Updates <https://galaxyproject.org/news/2019-02-galaxy-update/#doc-hub-and-training-…>, including *GO enrichment analysis* and *Age prediction using machine learning*. - ToolShed contributions <https://galaxyproject.org/news/2019-02-galaxy-update/#toolshed-contributions> . - New releases <https://galaxyproject.org/news/2019-02-galaxy-update/#releases> of galaxy-lib and Planemo. - And a bunch of other news <https://galaxyproject.org/news/2019-02-galaxy-update/#other-news> too. If you have anything to add to next month's newsletter, then please send it to outreach(a)galaxyproject.org. Thanks, Dave C on behalf of, well, everyone -- https://galaxyproject.org/ https://usegalaxy.org/

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Vote Now: GCC2019 Training Topics
by Dave Clements 28 Jan '19

28 Jan '19

Hello all, The next 2019 Galaxy Community Conference (GCC2019) <https://galaxyproject.org/events/gcc2019/> will be in Freiburg (Germany) in July. This year the program is specifically aimed at drawing in more Galaxy end-users, including for training. We are really interested it what you would like to learn. *Please take a few minutes to decide <https://galaxyproject.org/events/gcc2019/training/#training-topic-votes> and then vote which training should be offered during GCC2019 <https://goo.gl/forms/iaY5AezdFpyJ0ETh2>! *If there is *any* chance that you will attend then we want to hear from you. *Topic voting closes 4 February.* The Training schedule, including instructors, will be published before early registration opens. GCC2019 <https://galaxyproject.org/events/gcc2019/> will be held 1-6 July in Freiburg, Germany. If you work in data-intensive biomedical research, there is no better place than GCC2019 to present your work and to learn from others. Thanks, and see you in Freiburg The GCC2019 Organizers <https://galaxyproject.org/events/gcc2019/organizers/> -- https://galaxyproject.org/ https://usegalaxy.org/

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January 2019 Galactic News: Events (Admin Training, PAG, GSOC, GCC, GalaxyAdmins), Platforms, Pubs, Jobs, COTM!, Doc, Training, Tools, Releases and more!
by Mo Heydarian 04 Jan '19

04 Jan '19

Hello All, Happy New Year! The *January 2019 Galactic News* is here! This is a summary of what is going on in the Galaxy community. Here's what's happening: - Event News <https://galaxyproject.org/news/2019-01-galaxy-update/#event-news> - 2019 Galaxy Admin Training: Registration is still open! <https://galaxyproject.org/news/2019-01-galaxy-update/#2019-galaxy-admin-tra…> - Training topic nomination for GCC2019 Training extended through 15 January! <https://galaxyproject.org/news/2019-01-galaxy-update/#gcc2019-training-topi…> - Galaxy will be at the 2019 Plant and Animal Genome (PAG) conference <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxy-pag-2019> - Galaxy needs your Google Summer of Code Project suggestions <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxy-needs-your-goo…> - And GalaxyAdmins needs your topic suggestions <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxyadmins-needs-yo…> - 80 new publications <https://galaxyproject.org/news/2019-01-galaxy-update/#publications>, including several spectacular ones - Some most excellent Galaxy Platform News <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxy-platforms-news>, including the *EGI Marketplace*. - The Contributor of the Month is ... Simon Gladman <https://galaxyproject.org/news/2019-01-galaxy-update/#new-galactic-blog-pos…> ! - 17 Open positions <https://galaxyproject.org/news/2019-01-galaxy-update/#whos-hiring> in 6 countries on 3 continents. - Doc, Hub, and Training Updates <https://galaxyproject.org/news/2019-01-galaxy-update/#doc-hub-and-training-…> covering RNA-Seq visualizations, BlockClust, cloud storage, cancer proteogenomics, and some introductory videos - ToolShed contributions <https://galaxyproject.org/news/2019-01-galaxy-update/#toolshed-contributions> - New releases <https://galaxyproject.org/news/2019-01-galaxy-update/#releases>: - Tripal Galaxy - connect Galaxy to your online database - BioBlend - a Python API for Galaxy and CloudMan - Planemo - utilities for building tools for Galaxy - And a bunch of other news <https://galaxyproject.org/news/2019-01-galaxy-update/#other-news> too See the newsletter for all of the details! Thanks for using Galaxy! Cheers, Mo Heydarian, on behalf of Galaxy

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December Galactic News
by Dave Clements 03 Dec '18

03 Dec '18

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November 2018 Galactic News: Platforms Directory; new events, pubs, blog posts, servers, tools and releases!
by Mo Heydarian 01 Nov '18

01 Nov '18

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Galaxy 18.09 Release
by Dannon Baker 29 Oct '18

29 Oct '18

We are pleased to announce the *release of Galaxy 18.09 <https://docs.galaxyproject.org/en/release_18.09/releases/18.09_announce.html>*. A few release highlights are: <http://localhost:8095/news/2018-9-galaxy-release/#extensive-workflow-enhanc…> Extensive Workflow Enhancements Workflows got a lot of love this time around, with new runtime parameters for subworkflows, exposed workflow versions, and zoom capability in the editor, to name a few. There were also a number of usability enhancements including better labeling, links, overhauled workflow import interfaces, and many more. <http://localhost:8095/news/2018-9-galaxy-release/#group-tags> Group Tags Galaxy now contains powerful new features for multiple factor analysis of collections of datasets. The concept of group tags has been added to Galaxy. These are a special class of tags that describe key-value pairs that can be attached to the contents of a collection during upload or using collection operation tools. These tags can describe multiple sets of variables for the contents of a collection. Once set, these tags can be consumed intelligently by tools that need to divide collections into multiple overlapping factors or sets of datasets. A special thanks to @mvdbeek for devising and implementing this approach. <http://localhost:8095/news/2018-9-galaxy-release/#python-3-beta-support> Python 3 Beta Support After almost 3 years of work and more than 100 pull requests, we are proud to announce the Beta-stage support for running Galaxy under Python 3. Lint, unit, API, framework, integration and Selenium tests all pass, time for you to give it a try and report any bug you find! Please see the full release notes <https://docs.galaxyproject.org/en/release_18.09/releases/18.09_announce.html> for more information, including how to upgrade today! *Thanks for using Galaxy!*

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GX-2018-0006 - Unauthorized File System Operations via New Upload API
by John Chilton 04 Oct '18

04 Oct '18

DESCRIPTION A high severity security vulnerability was recently discovered in Galaxy 18.05's new upload API by the Galaxy Committers Team. Anyone with a Galaxy account can exploit this vulnerability to read and write arbitrary files on the Galaxy host accessible by the system user Galaxy runs as. This is possible due to insecure handling of tar file extraction. This vulnerability has been assigned the disclosure ID GX-2018-0006. AFFECTED VERSIONS This vulnerability affects Galaxy version 18.05 only (and the current development branch). IMPACT Administrators of Galaxy 18.05 servers should patch immediately. Galaxy servers running versions of Galaxy older than 18.05 are unaffected by this problem. The fix sanitizes the contents of tar files during upload while extracting them. INSTRUCTIONS The fixes are available on the `release_18.05` branch in the Galaxy GitHub repository[2]. You can simply `git pull` or use your normal update procedure to get the changes. For the changes to take effect, YOU MUST RESTART ALL GALAXY SERVER PROCESSES. --John Chilton (on behalf of the Galaxy Committers) [1] https://github.com/galaxyproject/galaxy/blob/dev/SECURITY_POLICY.md [2] https://github.com/galaxyproject/galaxy/

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October 2018 Galactic News: SACNAS Workshops, European Galaxy Days, Admin Training; new Pubs, Public Servers, Job postings, and Blog posts!
by Mo Heydarian 01 Oct '18

01 Oct '18

Hello All, The October 2018 Galactic News <https://galaxyproject.org/news/2018-10-galaxy-update/> highlights what’s going on in the Galaxy this month, including: - Galactic Events: - 2018 SACNAS Workshops <https://galaxyproject.org/news/2018-10-galaxy-update/#2018-sacnas-pre-confe…>,10 October, USA - European Galaxy Days <https://galaxyproject.org/news/2018-10-galaxy-update/#european-galaxy-days-…>, 19 - 20 November, Germany - 2019 Galaxy Admin Training <https://galaxyproject.org/news/2018-10-galaxy-update/#2019-galaxy-admin-tra…>, 28 January - 1 February, USA - Other events <https://galaxyproject.org/news/2018-10-galaxy-update/#upcoming-events> across the world. - Galactic Blog <https://galaxyproject.org/news/2018-10-galaxy-update/#new-galactic-blog-pos…> : - Contributor of the Month: Yvan Le Bras <https://galaxyproject.org/news/2018-10-galaxy-update/#new-galactic-blog-pos…> - Tutorial of the month: “From Peaks to Genes” <https://galaxyproject.org/news/2018-10-galaxy-update/#new-galactic-blog-pos…> - Highlight: Hybrid Training delivering to far-reaching venues <https://galaxyproject.org/news/2018-10-galaxy-update/#new-galactic-blog-pos…> - New: - 200 publications <https://galaxyproject.org/news/2018-10-galaxy-update/#publications> - Public Galaxy Servers <https://galaxyproject.org/news/2018-10-galaxy-update/#public-galaxy-server-…>: MPDS-DM - Galactic Job Postings <https://galaxyproject.org/news/2018-10-galaxy-update/#whos-hiring> - Toolshed contributions <https://galaxyproject.org/news/2018-10-galaxy-update/#tools> - Releases <https://galaxyproject.org/news/2018-10-galaxy-update/#releases> of GVL 4.4.0, Planemo 0.55.0, and galaxy-lib. - And other news <https://galaxyproject.org/news/2018-10-galaxy-update/#other-news>. See the newslette <https://galaxyproject.org/news/2018-10-galaxy-update/>r for all of the details! Thanks for using Galaxy! Cheers, Mo, on behalf of Galaxy

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September 2018 News of the Galaxy
by Dave Clements 13 Sep '18

13 Sep '18

Hello all, The *September 2018 Galactic News* is here! This is a summary of what is going on in the Galaxy community. Here's what's happening: - Events - 2018 SACNAS Workshops <https://galaxyproject.org/news/2018-09-galaxy-update/#2018-sacnas-pre-confe…> - European Galaxy Days <https://galaxyproject.org/news/2018-09-galaxy-update/#european-galaxy-days-…>, 19-20 November, Freiburg, Germany - All upcoming events <https://galaxyproject.org/news/2018-09-galaxy-update/#upcoming-events> - New: - 80 publications <https://galaxyproject.org/news/2018-09-galaxy-update/#publications> - Galactic Blog entry: Contributor of the Month: Carrie Ganote <https://galaxyproject.org/news/2018-09-galaxy-update/#contributor-of-the-mo…> - Public Galaxy Server News <https://galaxyproject.org/news/2018-09-galaxy-update/#public-galaxy-server-…>: epiGeEC and MetaCentrum - ToolShed contributions <https://galaxyproject.org/news/2018-09-galaxy-update/#toolshed-contributions> - Hub and Documentation updates <https://galaxyproject.org/news/2018-09-galaxy-update/#hub-and-doc-updates> - CloudBridge v1 <https://galaxyproject.org/news/2018-09-cloudbridge-v1-release/> has been released! - Releases <https://galaxyproject.org/news/2018-09-galaxy-update/#releases> - And other news <https://galaxyproject.org/news/2018-09-galaxy-update/#other-news> too If you have anything to add to next month's newsletter, then please send it to outreach(a)galaxyproject.org. Thanks, Dave C on behalf of the Galaxy Community -- https://galaxyproject.org/ https://usegalaxy.org/

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