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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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August Galaxy News: GCC2019, Online GTN CoFest, new pubs, servers, tools...
by Dave Clements 02 Aug '18

02 Aug '18

Hello all, After a two-month hiatus, the August 2018 Galactic News <https://galaxyproject.org/galaxy-updates/2018-08/> is out! Here are some of the highlights: - GCCBOSC 2018 <https://galaxyproject.org/galaxy-updates/2018-08/#gccbosc-2018-is-done> has come and gone, *and the numbers were impressive* - GCC2019 <https://galaxyproject.org/galaxy-updates/2018-08/#2019-galaxy-community-con…> will be held in Freiburg, Germany, 1-6 July - What about BOSC? <https://galaxyproject.org/galaxy-updates/2018-08/#what-about-bosc>, you ask - Other event news: - GTN CoFest on Metagenomics Training Material <https://galaxyproject.org/galaxy-updates/2018-08/#gtn-cofest-on-metagenomic…>, 17 August, *online* - 2018 SACNAS Workshops <https://galaxyproject.org/galaxy-updates/2018-08/#2018-sacnas-workshops> - European Galaxy Days <https://galaxyproject.org/galaxy-updates/2018-08/#european-galaxy-days-19-2…>, 19-20 November, Freiburg, Germany - Gateways 2018 <https://galaxyproject.org/galaxy-updates/2018-08/#gateways-2018> early bird deadline *is Monday*. - Other Upcoming events <https://galaxyproject.org/galaxy-updates/2018-08/#upcoming-events> (on three continents in 6 countries) - Christophe Caron, 1968-2018 <https://galaxyproject.org/galaxy-updates/2018-08/#christophe-caron-1968-2018> - New: - 417 publications <https://galaxyproject.org/galaxy-updates/2018-08/#publications> (that's 3 month's worth) - Two Galactic Blog entries <https://galaxyproject.org/galaxy-updates/2018-08/#new-galactic-blog-entries>, including the first ever *Contributor of the Month* posting. - Public Galaxy Server News <https://galaxyproject.org/galaxy-updates/2018-08/#public-galaxy-server-news>: ProteoRE - ToolShed contributions <https://galaxyproject.org/galaxy-updates/2018-08/#toolshed-contributions> - Hub and Documentation updates <https://galaxyproject.org/galaxy-updates/2018-08/#hub-and-doc-updates> - Releases <https://galaxyproject.org/galaxy-updates/2018-08/#releases> of Galaxy, Planemo, galaxy-lib, ephemeris, and sequence_utils. - And other news <https://galaxyproject.org/galaxy-updates/2018-08/#other-news> too See the newsletter <https://galaxyproject.org/galaxy-updates/2018-08/> for the full story. Thanks for using Galaxy! -- https://galaxyproject.org/ https://usegalaxy.org/

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The Galaxy release 18.05 is out
by Martin Čech 23 May '18

23 May '18

Dear Community, We are happy to release Galaxy 18.05. Many thanks to committers and you, the community. Enjoy the on time release and please let us know if you face any issues. The release notes are available at https://docs.galaxyproject.org/en/release_18.05/releases/18.05_announce.html Thanks for using Galaxy! Martin, on behalf of the Galaxy committers

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GCCBOSC 2018 Early Registration Ends this Friday (May 11)
by Dave Clements 07 May '18

07 May '18

Hi All, Just a reminder that early registration for the Galaxy Community's biggest annual gathering ends this Friday. You can also register for housing and childcare too. https://galaxyproject.org/events/gccbosc2018/register/ https://galaxyproject.org/events/gccbosc2018/venue/#housing https://galaxyproject.org/events/gccbosc2018/childcare/ Hope to see you there, Dave C on behalf of the GCCBOSC 2018 Organizing Committee -- https://gccbosc2018.sched.com/ https://galaxyproject.org/ https://usegalaxy.org/

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