- galaxy-announce - lists.galaxyproject.org

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/

1 0

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/

1 0

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

1 0

March Galaxy News: GCCBOSC oral presentations due in 2 weeks, plus lots more
by Dave Clements 01 Mar '18

01 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/

1 0

GCCBOSC 2018 Abstract Submission & Early Registration are Open
by Dave Clements 20 Feb '18

20 Feb '18

Hello all, We are pleased to announce that abstract submission and early registration for GCCBOSC2018 <https://gccbosc2018.sched.com/> are now open. - Submit an abstract <https://easychair.org/conferences/?conf=gccbosc2018> (oral presentation abstracts due March 16) - Register <https://gccbosc2018.eventbrite.com/> - Book conference housing <https://gccbosc2018housing.eventbrite.com/> GCCBOSC 2018 <https://gccbosc2018.sched.com/> will be held 25-30 June in Portland, Oregon, United States. This brings the 2018 Galaxy Community Conference and the Bioinformatics Open Source Conference together into a unified week-long event. If you work in open source life science or data-intensive biomedical research, then there is no better place than GCCBOSC 2018 to present your work and to learn from others. Events GCCBOSC <https://gccbosc2018.sched.com/> starts with two days of training <https://gccbosc2018.sched.com/overview/type/C.x+Training+-+All> with a wide range of topics nominated and selected by our communities. Training is followed by a two day meeting, with joint and parallel tracks, featuring oral presentations, posters, demos, lightning talks, birds-of-a-feather and invited keynotes <https://galaxyproject.org/events/gccbosc2018/keynotes/>from Fernando Pérez <https://galaxyproject.org/events/gccbosc2018/keynotes/#bosc-gcc-joint-keyno…> of the Berkeley Institute for Data Science <https://bids.berkeley.edu/> and Project Jupyter <http://jupyter.org/>, and Tracy K. Teal <https://galaxyproject.org/events/gccbosc2018/keynotes/#bosc-2018-keynote-tr…> of The Carpentries. The week finishes with *CollaborationFest <https://galaxyproject.org/events/gccbosc2018/collaboration/> Core* and *Encore*, two or four days of collaborative work on code, documentation, training and challenging data analysis problems. Abstract Submission BOSC and GCC are now accepting abstracts <https://easychair.org/conferences/?conf=gccbosc2018> for oral presentations, posters, demos, and lightning talks. We are using EasyChair <https://easychair.org/> for submissions. If you don't already have an account, you'll need to create one. *The deadline for oral presentations is rapidly approaching (March 16) so plan to submit your abstracts soon.* Registration Register now <https://gccbosc2018.eventbrite.com/> to take full advantage of early registration discounts <https://galaxyproject.org/events/gccbosc2018/register/> for students/post-docs (75% off full price), non-profits (67%) and industry (50%). Early registration rates for students and post-docs average $66 / day. Conference Housing Official conference housing <https://gccbosc2018housing.eventbrite.com/> for GCCBOSC 2018 is in Reed residence halls. Rooms are within easy walking distance of all conference venues. Room prices per night drop the longer the stay. If you prefer to stay elsewhere, Reed College has a list of recommended hotels <https://www.reed.edu/accommodations.html>, many offering a discount for those attending events at Reed. Travel Fellowships Both OBF and the Galaxy Community Fund Board are offering fellowships to attend GCCBOSC 2018: - OBF Travel Fellowships <https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md>, deadline is April 15. - GCC2018 Fellowships <https://galaxyproject.org/news/2018-02-20-gcc-fellowships/>, first deadline is March 16. See you in Portland! The GCCBOSC 2018 Organizers <https://galaxyproject.org/events/gccbosc2018/organizers> -- https://galaxyproject.org/ https://usegalaxy.org/

1 0

Galaxy News: GCCBOSC Training Topic Voting closes Wednesday!
by Dave Clements 30 Jan '18

30 Jan '18

1 0

GCCBOSC 2018 Training Topic Voting is now open
by Dave Clements 22 Jan '18

22 Jan '18

Hello all, Voting is now open <http://bit.ly/gccbosc2018-vote> on what training topics <https://galaxyproject.org/events/gccbosc2018/training/> will be offered at GCCBOSC 2018 <https://gccbosc2018.sched.com/>. Your vote <http://bit.ly/gccbosc2018-vote> will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters. *Topic voting closes January 31.* The Training schedule, including instructors, will be published before early registration opens. GCCBOSC2018 <https://gccbosc2018.sched.com/> will be held 25-30 June in Portland, Oregon, United States. It will feature two days of training: the second of which is multi-track and will feature content for both the BOSC and Galaxy communities. Workshops will be hands-on and participants will be strongly encouraged to bring a laptop and follow along. If you work in data-intensive biomedical research, there is no better place than GCCBOSC 2018 to present your work and to learn from others. Thanks, and see you in Portland! The GCCBOSC 2018 Organizers <https://galaxyproject.org/events/gccbosc2018/organizers> -- https://galaxyproject.org/ https://usegalaxy.org/

1 0

January Galactic News
by Dave Clements 05 Jan '18

05 Jan '18

1 0

GCCBOSC 2018 Training Topic Nominations are Open!
by Dave Clements 14 Dec '17

14 Dec '17

Hello all, This email in 5 words: *Nominate a training topic now <http://bit.ly/gccbosc2018-tr-nom>!* Or, the longer version: The joint 2018 Galaxy Community and Bioinformatics Open Source Conferences <https://gccbosc2018.sched.com/> start with training and *the training topics are determined by you*. Please take a few minutes to consider what you would like to learn (or teach) at GCCBOSC2018. Any topic(s) of interest to these communities can be *nominated <http://bit.ly/gccbosc2018-tr-nom>.* GCCBOSC2018 <https://gccbosc2018.sched.com/> will be held 25-30 June in Portland, Oregon, United States, and will feature two days of training - the second of which is multi-track and will feature content for both the BOSC and Galaxy communities. Nominations can cover a wide range of topics. For example: - How to use open source software using just a web browser (e.g., Intro to Using Galaxy) - How to use software packages (The Newbie's Guide to BioRuby) - Advanced applications of software (Genome Assembly with Galaxy, or Proteomics with BioPython) - Software installation and configuration (Tool Wrapping for Galaxy, or Using CloudLaunch) - Open source community (Building a Curation Community using Apollo, or Training using the Galaxy Training Network) *These are only examples.* If you are looking for ideas, see topics nominated for GCC2017 <https://docs.google.com/document/d/1jyCndVqfXx-HsyFJ4hjaK075vDbPM1kE58qO2lJ…> , GCC2016 <http://bit.ly/gcc2016noms>, GCC2015 <http://bit.ly/gcc2015vote>, and the Galaxy Events page <https://galaxyproject.org/events/>, which lists what training the community is offering outside of GCCs. *Training is not limited to Galaxy-related topics. Don't be afraid to think inside the BOSC!* Basically, if you think our communities will be interested in a topic, then please nominate it <http://bit.ly/gccbosc2018-tr-nom>! Nominated topics will be published <https://galaxyproject.org/events/gccbosc2018/training/> as they come in. *Topic Nominations close January 7*. Topics will be compiled into a uniform list by the GCCBOSC2018 organizers, and then voted on by the community starting one week later. Looking forward to seeing you in Portland! Dave Clements, on behalf of the GCCBOSC 2018 Organizers -- https://galaxyproject.org/ https://usegalaxy.org/

1 0

December 2017 News of the Galaxy
by Dave Clements 07 Dec '17

07 Dec '17

1 0