August 2017 Galaxy News

Galaxy News

Welcome to the August 2017 Galactic News, a summary of what is going on in the Galaxy community. If you have anything to add to next month's newsletter, then please send it to outreach@galaxyproject.org.

GCC2018: Portland, Oregon, United States, June 25-30

GCC2018 will be colocated with BOSC 2018 in Portland, Oregon

We are pleased to announce that the 2018 Galaxy Community Conference (GCC2018) and the Bioinformatics Open Source Conference 2018 (BOSC2018) are joining together for a unified event to be held in Portland, Oregon, United States, June 25-30, 2018. The event will feature two days of training, a two day meeting, and finish with two days of intense collaboration at the OBF Codefest, and Hack the Galaxy: Dev and Data. The meeting will feature joint and parallel sessions, and shared keynotes, poster and demo sessions, and social events. Colocating GCC and BOSC will bring together the widest possible community of bioinformatics developers and practitioners into a single place. At this event the whole will be greater than the sum of the parts.

The event is organized by Oregon Health & Science University (OHSU) and will be held at Reed College, a small liberal arts college in Portland. Portland is a vibrant city in the American Northwest, close to the Cascade Mountains, the Oregon Coast, and the Columbia River.

GCC2017 is Done!

GCC2017 was held 26-30 June in Montpellier, France. The eighth global gathering of the Galaxy community featured two days of Hack the Galaxy, two days of training, and a two day community conference. Most training materials, slides, and posters are now available online. Slides and posters are also being uploaded to the F1000 Galaxy Channel. Take a look.

Two summaries of GCC2017 are available online:


Preconference data workshops at 2017 SACNAS Meeting

Software Carpentry

Data Carpentry

CyVerse

Galaxy

Galaxy (and CyVerse and the Carpentries) at 2017 SACNAS Meeting

If you are attending the 2017 SACNAS meeting in Salt Lake City in October, then please consider signing up for one of these preconference workshops:

Software and Data Carpentry

Data Platforms for Life Science Researchers

Registration is free but space is limited. You are strongly encouraged to register soon. Both workshops are held October 18, the day before SACNAS starts.

Register Now

Plese note: The Galaxy Community Fund is augmenting SACNAS Travel Scholarships awards for the first ~ 28 scholarship recipients that register for these workshops. The additional funds will cover an extra night's lodging for scholarship recipients, enabling you to arrive the day before the workshops. Funds are limited, and once the funds are allocated, they are gone. (You must hve received a SACNAS Travel Scholarship to be eligible.)

Galaxy @ ISMB/ECCB/BOSC 2017: Slides and posters are available

Galaxy at ISMB/ECCB/BOSC 2017Slides and posters)

If you missed all the Galaxy @ ISMB/ECCB 2017 & BOSC 2017 then don't, um, fret! Most slides and posters are available online)

See you next year in Chicago!

All events

There are a plenitude of Galaxy related events coming up in the next few months:

Date Topic/Event Venue/Location Contact
August 2nd 2017 Genome assembly using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
August 9th 2017 Introduction to Galaxy Workshop University of Glasgow, Glasgow, United Kingdom David Meltzer
September 1st 2017 The Galaxy Bioinformatics Platform: learning to use Galaxy for RNA-seq analysis [hub page] Genome 10K and Genome Science, Earlham Institute, Norwich, United Kingdom Training offered by GTN MemberNicola Soranzo, Graham Etherington
September 13th 2017 RNA-Seq analysis using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
September 25th 2017 Computational Genomics and RNA Biology Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany Training offered by GTN Membercompgen@mdc-berlin.de
October 3rd 2017 Introduction to Galaxy & the Genomics Virtual Laboratory Melbourne Bioinformatics, Carlton, Victoria, Australia Training offered by GTN Member
October 4th 2017 RNA-Seq Differential Gene Expression Analysis using Galaxy & the GVL Melbourne Bioinformatics, Carlton, Victoria, Australia Training offered by GTN Member
October 4th 2017 A primer for RNA-Seq processing, interpreting and visualization University of Freiburg, Freiburg Germany Steve Hoffmann, Olaf Wolkenhauer, Wolfgang Hess
October 5th 2017 Variant Calling with Galaxy & the GVL for beginners Melbourne Bioinformatics, Carlton, Victoria, Australia Training offered by GTN Member
October 18th 2017 SACNAS 2017 Pre-Conference Workshops 2017 SACNAS, Salt Lake City, Utah, United States Training offered by GTN MemberCamille Avestruz, Tracy Teal, Joslynn Lee, Dave Clements
October 23rd 2017 Gateways 2017 University of Michigan, Ann Arbor, Michigan, United States Enis Afgan
October 23rd 2017 The Future Development of Bioinformatics in Germany and Europe ZiF, Bielefeld University, Bielefeld, Germany Rolf Backofen, Björn Grüning
October 23rd 2017 Analyse avancée de séquences Carreire de l'Université Bordeaux Segalen, Bordeaux, France Aurélien Barré, Raluca Uricaru, Benjamin Dartigues
January 8th 2018 European Galaxy Administrator Workshop Oslo, Norway Training offered by GTN Member

See the Galaxy Events Google Calendar for details on other events of interest to the community.


New Publications

298 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy CiteULike Group in June and July.

Some highlights from the recently added publications:

Publication Topics

# Tag # Tag # Tag # Tag
167 methods 55 workbench 55 usepublic 35 usemain
20 uselocal 20 isgalaxy 19 refpublic 16 tools
15 reproducibility 9 cloud 8 other 7 unknown
4 shared 2 howto 1 visualization 1 usecloud

Who's Hiring

[Please Help! Yes you!]

The Galaxy is expanding! Please help it grow.

Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the Galaxy News feed and include it in next month's update.



Public Galaxy Server News

There are over 90 publicly accessible Galaxy servers and six semi-public Galaxy services. Here's what happened with them in May

Galaxy Integrated Omics (GIO)

Usegalaxy.org

  • Jupyter Interactive Environments now run on Jetstream cloud via Docker Swarm and Galaxy Swarm Manager.

New Public Galaxy Servers

ABiMS

ABiMS

ABiMS Galaxy supports general purpose genomics analysis, featuring many standard tools plus many additional tools. However, we are specialized in RNASeq with reference and de novo RNASeq. Anyone with a professional/institutional email address can request an account. The server is only available for registered users, and the default quota for new users is 20GB but can be extended on request. Email support is available. ABiMS is supported by CNRS, UPMC, BioGenOuest, IFB, and Station Biologique de Roscoff


Tools

ToolShed Contributions

Galaxy ToolShed

Tool Shed contributions from June and July.

Releases

Galaxy TourBuilder

The Galaxy TourBuilder records your Galaxy analysis in real-time and creates a Galaxy Tour for you - automatically! You can edit the tour simultanously, replay the tour while you are analysing your data and much more!

Check out the video to get a taste of what it can do for you.

This extension is available under the name Galaxy Tour Builder in the Chrome Web Store, the Mozilla (Firefox) Add-on website, and the Opera add-ons website. Credits

This project was initiated during the Swiss-Germany Galaxy Days a while ago in Freiburg by Dannon Baker and William Durand. During GCC 2017 Florian Eggenhofer, Matthias Bernt, Bérénice Batut and Clemens Blank have picked up this project and with tramendous help from TailorDev so a first version could be released.

Planemo 0.41.0 - 0.44.0

Planemo

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. These releases included numerous fixes and enhancements.

See GitHub for details.

galaxy-lib 17.9.0-3

galaxy-lib is a subset of the Galaxy core code base designed to be used as a library. This subset has minimal dependencies and should be Python 3 compatible. It's available from GitHub and PyPi.

This set of revisions includes:

  • Bring in latest Galaxy dev changes.
  • Implement support for building Singularity mulled containers.
  • Implement mulled version 2 package hashing.
  • Fix default namespace for mulled operations from mulled to biocontainers.

gops 1.1.0

The Galaxy Operations Python Package now provides utilities for working with GFF files thanks to @bgruening and @nsoranzo.

Earlier Releases

Other packages that have been released in the prior 4 months.

May 2017 Galaxy Release (v 17.05)

GalaxyProject

Tag your datasets to keep track of where computed datasets came from
# Tags are propogated
in histories

Drag and drop with Galaxy Histories and Tools
Drag and drop in Galaxy 17.05

The Galaxy Committers published the 17.05 release of Galaxy in May.

Tag your data with propagating hashtags

  • Large Galaxy histories used to be messy. Hashtags make it easy to track dataset (and collection) relationships.
  • These two movies (both under a minute) explain how to use this with datasets and with collections.
  • Learn more about Galaxy histories in our updated tutorial.

Drag & Drop datasets into tool inputs

  • Interface now allows dragging datasets from history panel into the content selectors of the tool form.
  • Implemented in Pull Request 3871.

Upload directly to a collection

  • You can now bypass the history manipulation and upload your data straight into a collection for convenience.
  • Learn more about collections and how to use them in a new tutorial.

We extend special thanks to the 64 New Contributors to Galaxy in the past year.

Additionaly there are New Configuration Options and New Datatypes sections.

Galaxy Docker Image 17.05

The Galaxy Docker project has seen a new release, following Galaxy 17.05. Major features are an additional Docker compose setup with SLURM and HT-Condor deployments, BioContainers integration and much more automatic testing.

And

Parsec 1.0.0 - 1.0.2

Parsec is a newly released set of command-line utilities to assist in working with Galaxy servers. It uses automatically generated wrappers for BioBlend functions. Manage histories, launch workflows, and more, all from the command line. The README includes several examples.

BioBlend 0.9.0

BioBlend is a Python library for interacting with CloudMan and Galaxy‘s API. BioBlend makes it possible to script and automate the process of cloud infrastructure provisioning and scaling via CloudMan, and running of analyses via Galaxy.

See the release notes for what's new in release 0.9.0.

Galaxy CloudMan 17.05 on AWS

A new release of Galaxy CloudMan is available on the Amazon Web Services cloud infrastructure. This release includes Galaxy 17.05, an updated tool list, and Slurm configuration changes to improve job performance. To get started, vist https://beta.launch.usegalaxy.org/ or take a look at the Getting Started guide.

CloudLaunch

Technically, the all-new Galaxy CloudLaunch service has been in public beta since February but keep in mind that it will replace the current CloudLaunch service eventually so give it a try and let us know how it performs for you.

CloudBridge 0.2.0

CloudBridge aims to provide a simple layer of abstraction over different cloud providers, reducing or eliminating the need to write conditional code for each cloud. It is currently under development and is in an Alpha state. Release 0.2.0 includes several fixes and enhancements.

And the rest ...

Other Galaxy packages that haven't had a release in the past four months can be found on GitHub.


Other News

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