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March 2018

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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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March Galaxy News: GCCBOSC oral presentations due in 2 weeks, plus lots more
by Dave Clements 02 Mar '18

02 Mar '18

Hello all, The March 2018 Galaxy News <https://galaxyproject.org/galaxy-updates/2018-03/> brings more news than usual, with much of it about upcoming meetings, including GCCBOSC, and continental meetings in Europe and Africa. - *Lots* of GCCBOSC 2018 news <https://galaxyproject.org/galaxy-updates/2018-03/#gccbosc-2018>: - Abstract submission, registration & housing are open <https://galaxyproject.org/galaxy-updates/2018-03/#abstract-submission-regis…> - *Oral presentation abstracts due March 16 <https://easychair.org/conferences/?conf=gccbosc2018>* - Training Schedule set <https://galaxyproject.org/galaxy-updates/2018-03/#training-schedule-set> - 17 topics in 22 sessions over two days covering the full spectrum of open source bioinformatics - We are pleased to announce two of the keynote speakers <http://localhost:8080/galaxy-updates/2018-03/#keynote-speakers>: - Fernando Pérez, of the Berkeley Institute for Data Science, University of California Berkeley and Project Jupyter - Tracy K. Teal, of the Carpentries and the *Journal for Open Scource Software* - Sponsors <https://galaxyproject.org/galaxy-updates/2018-03/#gccbosc-2018-sponsors> : - F1000Research <https://galaxyproject.org/galaxy-updates/2018-03/#f1000research> - Technology Association of Oregon <https://galaxyproject.org/galaxy-updates/2018-03/#technology-association-of…> - Call for sponsors <https://galaxyproject.org/galaxy-updates/2018-03/#call-for-sponsors> - *Continental* community meetings: - *Europe, 14-16 March, Freiburg* <https://galaxyproject.org/galaxy-updates/2018-03/#elixir-galaxy-community-k…> - *Africa, 3-5 April, Cape Town* <https://galaxyproject.org/galaxy-updates/2018-03/#galaxy-africa-3-5-april-c…> - Apply for a Conference Fellowship <https://galaxyproject.org/galaxy-updates/2018-03/#conference-fellowships> *by 10 March*. - Upcoming events <https://galaxyproject.org/galaxy-updates/2018-03/#upcoming-events> (on four continents) - New: - Galactic Blog post from Arun Decano: Coding in the Winter Wonderland: Galaxy Admin Training <https://galaxyproject.org/galaxy-updates/2018-03/#new-galactic-blog-entry-c…> - 133 publications <https://galaxyproject.org/galaxy-updates/2018-03/#publications> (including 5 highlighted ones) - Openings in 6 groups on 2 continents <https://galaxyproject.org/galaxy-updates/2018-03/#whos-hiring> - Public Galaxy Server News <https://galaxyproject.org/galaxy-updates/2018-03/#public-galaxy-server-news> (a new server and two updated ones) - ToolShed contributions <https://galaxyproject.org/galaxy-updates/2018-03/#toolshed-contributions> - Releases <https://galaxyproject.org/galaxy-updates/2018-03/#releases> of Planemo, Pulsar, and galaxy-lib. - And other news <https://galaxyproject.org/galaxy-updates/2018-03/#other-news> too See the newsletter <https://galaxyproject.org/galaxy-updates/2018-03/> for more. Hope to see you in Freiburg, Cape Town, and Portland! Dave C -- https://gccbosc2018.sched.com/ https://galaxyproject.org/ https://usegalaxy.org/

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