- galaxy-announce - lists.galaxyproject.org

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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May Galaxy News: GCCBOSC, Training Material Workshop, New pubs, jobs, ...
by Dave Clements 02 May '18

02 May '18

Hello all, The May 2018 Galactic News <https://galaxyproject.org/galaxy-updates/2018-05/> highlights what's going on in the Galaxy this month, including: - Lots of GCCBOSC 2018 news <https://galaxyproject.org/galaxy-updates/2018-04/#gccbosc-2018>: - *Early registration ends May 11 <https://galaxyproject.org/galaxy-updates/2018-05/#early-registration-ends-m…>* - Galaxy talks have been posted to the schedule <https://galaxyproject.org/galaxy-updates/2018-05/#gcc2018-schedule-posted> . - BOSC deadline for late-breaking lightning talks, demos and posters *is May 17 <https://galaxyproject.org/galaxy-updates/2018-05/#bosc-deadline-for-late-br…>* - Please welcome *Google Cloud <https://galaxyproject.org/galaxy-updates/2018-05/#gigascience-and-oxford-un…>* and *Advanced HPC <https://galaxyproject.org/galaxy-updates/2018-05/#advanced-hpc>* as GCCBOSC sponsors. *Both are offering goodies for conference participants.* - Other event news: - ELIXIR Workshop for Galaxy training material and skills improvement <https://galaxyproject.org/galaxy-updates/2018-05/#elixir-workshop-for-galax…> is 21-23 May. Register right now. - Galaxy Africa Report <https://galaxyproject.org/galaxy-updates/2018-05/#galaxy-africa-report> - Other Upcoming events <https://galaxyproject.org/galaxy-updates/2018-05/#upcoming-events> (on three continents in 6 countries) - New: - 132 publications <https://galaxyproject.org/galaxy-updates/2018-05/#publications> - Openings in 10 groups on 2 continents <https://galaxyproject.org/galaxy-updates/2018-05/#whos-hiring> - Public Galaxy Server News <https://galaxyproject.org/galaxy-updates/2018-05/#public-galaxy-server-news> : IRProfiler <https://galaxyproject.org/galaxy-updates/2018-05/#irprofiler> - ToolShed contributions <https://galaxyproject.org/galaxy-updates/2018-05/#toolshed-contributions> - Releases <https://galaxyproject.org/galaxy-updates/2018-05/#releases> of BioBlend and Starforge See the newsletter <https://galaxyproject.org/galaxy-updates/2018-05/> for the full story, and we hope to see you in Portland! Dave C on behalf of, well, everyone -- https://gccbosc2018.sched.com/ https://galaxyproject.org/ https://usegalaxy.org/

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April Galactic News: UseGalaxy.org gets some siblings, GCCBOSC and other event news; new pubs, servers, jobs, ...
by Dave Clements 11 Apr '18

11 Apr '18

Hello all, The April 2018 Galactic News <https://galaxyproject.org/galaxy-updates/2018-04/> highlights what's going on in the Galaxy (and it's actually quite cool). Take a look: - *UseGalaxy.eu and UseGalaxy.org.au Launched <https://galaxyproject.org/galaxy-updates/2018-04/#usegalaxyeu-and-usegalaxy…>* - Lots of GCCBOSC 2018 news <https://galaxyproject.org/galaxy-updates/2018-04/#gccbosc-2018>: - We are pleased to announce that Lucia Peixoto <https://galaxyproject.org/galaxy-updates/2018-04/#keynote-speakers> of Washington State University will be our third keynote speaker. - Please welcome *Google Cloud <https://galaxyproject.org/galaxy-updates/2018-04/#google-cloud>* as a GCCBOSC Platinum sponsor. - *GCC Lightning talk, poster and demo submissions are due by April 16 <https://galaxyproject.org/galaxy-updates/2018-04/#submit-gcc-lightning-talk…>* - Childcare for GCCBOSC <https://galaxyproject.org/galaxy-updates/2018-04/#childcare-at-gccbosc>! Space is limited, so register *now*. - Upcoming Events: - 2018 Big Genomics Data Skills Training course <https://galaxyproject.org/galaxy-updates/2018-04/#2018-big-genomics-data-sk…> - how to integrate genomic data analysis into undergraduate coursework - Gateways 2018 Call for Participation <https://galaxyproject.org/galaxy-updates/2018-04/#gateways-2018-call-for-pa…> - Upcoming events <https://galaxyproject.org/galaxy-updates/2018-04/#upcoming-events> (on four continents) - New: - 119 publications <https://galaxyproject.org/galaxy-updates/2018-04/#publications> (including 9 highlighted ones) - Openings in 9 groups on 2 continents <https://galaxyproject.org/galaxy-updates/2018-04/#whos-hiring> - Public Galaxy Server News <https://galaxyproject.org/galaxy-updates/2018-04/#public-galaxy-server-news> (a new server and an updated one too) - ToolShed contributions <https://galaxyproject.org/galaxy-updates/2018-04/#toolshed-contributions> - Releases <https://galaxyproject.org/galaxy-updates/2018-04/#releases> of Galaxy, Galaxy Docker, blend4j, and galaxy-lib - And other news <https://galaxyproject.org/galaxy-updates/2018-04/#other-news> too See the newsletter <https://galaxyproject.org/galaxy-updates/2018-04/> for the full story, and we hope to see you in Portland! Dave C, on behalf of the Galaxy -- https://gccbosc2018.sched.com/ https://galaxyproject.org/ https://usegalaxy.org/

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Release of Galaxy 18.01
by Martin Čech 19 Mar '18

19 Mar '18

Dear Galaxy Fans, The release of Galaxy 18.01 is out. Thanks to the Galaxy committers and you, our community! Full release notes: https://docs.galaxyproject.org/en/release_18.01/releases/18.01_announce.html *Highlights:* *Performance and User Experience Improvements* We made Galaxy more lively and responsive. Homepage, published workflows, published/saved histories, and data libraries should all load much faster now. Importing data from FTP will also take less of your time. *Web Server and Configuration* The default web server used by Galaxy has changed from Paste to uWSGI and the default configuration file for Galaxy is now config/galaxy.yml instead of config/galaxy.ini. To minimize the impact of this change on existing Galaxy instances, if a Galaxy has a galaxy.ini file configured, it will continue to use Paste by default unless additional steps are taken by the administrator *Dataset Collection Usability* This release has significantly improved the usability of Galaxy dataset collections. Dozens of improvements to collections have been made, some of the key highlights include: * Data library folders can now be sent to histories as a dataset collection. * Failed dataset collection elements can now be fixed using job re-running * Collections now appear with state and progress bars in the history panel and contained datasets are hidden by default * We added intuitive workflow post job actions for dataset collections * The web interface now supports collections with arbitrary nesting and size * More robust nametag discovery and propagation when using collections *Client Architecture* The architecture for the client code that powers the Galaxy user interface has been significantly overhauled. The code base has been converted to ES6, Yarn now powers the build and dependency management of the code, Prettier is now used to ensure consistent code formatting, and the VueJS framework has been integrated. *New BAM datatypes* Previously Galaxy only supported coordinate sorted BAM files by default (the bam datatype). In addition, this release of Galaxy now supports three new types of BAM: * qname_sorted.bam, that ensures that the file is queryname sorted (e.g. SO:queryname); * qname_input_sorted.bam, that can be used to describe the output of aligners which generally keep mate pairs adjacent * unsorted.bam, that makes no assumptions about the sort order of the file. *Experimental Job Caching* Galaxy can now be configured to allow users the option of skipping duplicated jobs if one with identical parameters has been previously executed and simply reuse the previously generated outputs. Thanks for using Galaxy! http://galaxyproject.org

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