Locked History Actions

GalaxyUpdates/2016_11

November 2016 Galaxy News

Galaxy News

Welcome to the November 2016 Galactic News, a summary of what is going on in the Galaxy community.

The big news this month is still a series of upcoming events:

If you have anything to include in the next News, please send it to Galaxy Outreach <outreach AT galaxyproject DOT org>.

Events

There are a wealth of events coming up. Here are some highlights, and a report on one from last month too.

Galaxy Australasia Meeting (GAMe 2017)

Galaxy Australasia Meeting 2017

GAMe 2017 will bring together biomedical researchers, bioinformaticians, infrastructure providers, and data producers from across Australia and Asia to share expertise across many levels.

This meeting features three distinct events:

Oral Presentation Abstracts Due 30 November

Accepted talks will be presented during the 2-day conference, 4-5 February. Talks are 15-20 minutes long and the meeting is single track.

Oral presentation abstract submission is open until 30 November 2016. Abstracts are limited to 250 words or less.

Poster Submission and Early Registration

Poster abstract submission is open until we run out of poster space. Abstracts are limited to 250 words or less. Poster abstracts are reviewed on a rolling basis and submitters will be notified of the decision within two weeks of the abstract’s submission date.

Early registration is open until 31 December. Register now and save up to 43% off regular registration rates. There are also scholarships available for eligible students and postdocs. The scholarship application deadline is 18 November.

Bioconda Contribution Fest, November 2-3, Online

BioConda and Galaxy

Our first Bioconda Contribution Fest will be on the 2-3 November! We will have an IRC channel (maybe gitter?) and a google hangout in place.

We will start with a short presentation of all ideas and try to create small groups to tackle problems small groups. I guess it's a good idea if you fork bioconda-recipes and get your own travis setup up and running so we avoid the travis bottleneck.

See the event page for ideas and more details.

European Galaxy Developer Workshop

https://www.france-bioinformatique.fr/en/evenements/EGDW2017
https://www.france-bioinformatique.fr/en/evenements/EGDW2017

Registration is now open for the European Galaxy Developer Workshop being held 16-19 January in Strasbourg, France.

During this 4 day course, attendees will learn how to integrate high-quality tools and visualisations into Galaxy using best practice guidelines and finally how to deploy them. The last day will be spent to learn how to configure a production ready Galaxy server. Moreover, at the end of this course you will have a profound knowledge about Docker and Conda.

Travel expenses and lodging need to be covered by each participant individually. ELIXIR-EXCELERATE and IFB (French Node) are covering the meeting costs.

Galaxy Admin Training, November 7-11, Salt Lake City, Utah

Galaxy Project Admin Training
November 7-11, 2016
University of Utah
Salt Lake City, Utah

There are still a few spaces left.

Galaxy Admin Training 2016 is a weeklong event offering basic and advanced sessions. It is being held in Salt Lake City, Utah, November 7-11, 2016, the week before Supercomputing 16 (SC16) meets in Salt Lake.

Basics Session: November 7-8

This two day basics session will introduce participants to what you need to know to get a Galaxy server up and running on a standalone server. You'll also learn how to extend your Galaxy with your own tools and tools from the community, and how to define reference data in your server.

Advanced Session: November 9-11

The three day advanced session will build on topics covered in the basics section. This session extends those topics, such as tool definition, and adds new ones, such as working with compute clusters and heterogeneous resources. The advanced workshop focuses on creating robust, high-performance Galaxy instances that take full advantage of available tools and compute and storage resources.

Report: Galaxy training material: A Contribution Fest beyond any expectations

On the 6 and 7th of October, the Galaxy Training Network had its first online Contribution Fest with an impressive amount of contributions and contributors! This was beyond any expectations!

  • 25 persons joined the Contribution Fest - a few of them had never contributed to an open source project on GitHub. Institutions like ELIXIR, de.NBI and IFB had persons contributing to the this Contribution Fest.

  • During the two days, more than 44 commits went into the master branch. 24 pull request were opened and 15 of them were merged. 5 Issues were closed and 5 created. 16 previously opened issues were used to plan the further direction of this initiative.
  • Before the Fest, 9 topics were available with different materials (hands-on tutorials, slides, …). During the two days, 1 new topic and 2 new tutorials were proposed, 2 slide decks were created and 7 tutorials were updated to follow our guidelines.
  • More than 350 messages were exchanged over the Gitter channel during these few days. A few video calls were made to explain the goals and the guidelines. One main discussion point was the slide format which we defined - we will rethink this and propose a new one soon - this should go hand in hand with the new Galaxy wiki system.

See the full report for more.

This Contribution Fest was fantastic and we learned a lot during these days. We would like to warmly thank all the participants. Great community effort!

Bérénice and Bjoern

Report: Swiss-German Galaxy Days

2016 Swiss German Galaxy Tour

Well over 30 people from all over Europe (not just Germany and Switzerland) attended the "Swiss German Galaxy Tour 2016" which took place over two days in Freiburg, Germany, mid October.

On the first day several talks highlighted new developments coming from the wide Galaxy community, including updates wrt training and tool development. Participants had a chance to show how they use Galaxy and how they have implemented Galaxy locally. Many took the opportunity to discuss their challenges. And it was great to see how quickly solutions emerged from the group of participants.

On the second, we tried a new hackathon format: A topic was presented with a short theoretical introduction. This was followed by 90 minutes of hacking and 15 minutes discussion. During the introduction a set of starting points was shown allowing the beginner to explore the topic and the advanced user to work on a real case. Three such mini hackathons were run covering: creating Conda packages, Galaxy tours, and creating Galaxy Docker flavors.

We would like to thank for the financial support we got from de.NBI ELIXIR and for all the help we got from the Galaxy team, especially for sending Dannon over to Europe. It was great to have him, and the event profited a lot from him.

We are looking forward to the next Swiss German Galaxy Tour.

Björn and Hans-Rudolf

All upcoming events

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

Bioconda Contribution Fest Analyse de données RNA-seq sous l’environnement Galaxy       Galaxy Project Admin Training Galaxy Australasia Meeting 2017

Date

Topic/Event

Venue/Location

Contact

November 2-3

Bioconda Contribution Fest

Around the world
Online

Björn Grüning

November 7-8

Galaxy Admin Training: Introduction

North America
Salt Lake City, Utah, United States

Training offered by GTN Member
Instructors

November 7-9

NGS & Cancer : Analyses ChIP-Seq

Workshop is full

Europe
Paris, France

Cancéropôle Île-de-France <communication@canceropole-idf.fr>

November 7-9

Tool deployment and sustainability in bioinformatics – fixed!

Europe
Bioinformatics for Human Health and Disease, Heidelberg, Germany

Bérénice Batut

November 8-20

Advanced Sequencing Technologies & Applications

Application deadline is July 15

North America
Cold Spring Harbor Laboratory, New York, United States

Training offered by GTN Member
Jeremy Goecks

November 9-11

Galaxy Admin Training: Advanced

North America
Salt Lake City, Utah, United States

Training offered by GTN Member
Instructors

November 11

Introduction to the GVL and Galaxy

Australia
University of Melbourne, Melbourne, Victoria, Australia

Training offered by GTN Member
VLSCI

November 15-16

Analyse de données RNA-seq sous l’environnement Galaxy

Europe
PRABI, Lyon, France

Contact

November 16

Quality Control of Next Generation Sequencing Reads

Europe
University of Aberdeen, Scotland, United Kingdom

Sophie Shaw <s.shaw@abdn.ac.uk>

November 16

Introduction to Galaxy Workshop

North America
University of Utah, Salt Lake City, Utah, United States

Training offered by GTN Member
Dave Clements

November 20-25

Ecole Bioinformatique AVIESAN

Europe
Station Biologique, Roscoff, France

Training offered by GTN Member
Email <ecole-bioinfo@aviesan.fr>

November 21

Pasteur_galaxy: An open and sustainable Galaxy instance for NGS data analysis

South America
ISCB-Latin America, Buenos Aires, Argentina

Oussama Souiai

November 21-23

Annotation of transposable elements

Europe
URGI, INRA Versailles, France

Contact

November 28 - December 2

Traitement des donnéesmétabolomiques sous Galaxy

Les pré-inscriptions sont ouvertes jusqu'au 15 juillet 2016

Europe
Station Biologique, Roscoff, France

Training offered by GTN Member
Contact <contact@workflow4metabolomics.org>

November 29

Genome Assembly and Annotation

Europe
University of Aberdeen, Scotland, United Kingdom

Sophie Shaw <s.shaw@abdn.ac.uk>

2017

January 14-18

Galaxy @ Plant & Animal Genome XXIV (PAG 2017)

North America
San Diego, California, United States

Dave Clements

January 16-19

European Galaxy Developer Workshop

Europe
Strasbourg, France

Training offered by GTN Member
Organisers <egdw2017.oc@groupes.france-bioinformatique.fr>

February 3-9

Galaxy Australasia Meeting (GAMe 2017)

Australia
University of Melbourne, Victoria, Australia

Training offered by GTN Member
Organisers

June 26-30

2017 Galaxy Community Conference (GCC2017)

Europe
Montpellier, France

Training offered by GTN Member
Organisers <gcc2017_organization@groupes.france-bioinformatique.fr>

Designates a training event offered by GTN Member

Designates a training event offered by GTN member(s)

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


New Publications

87 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy CiteULike Group in October.

Some highlights from last month:

Tagged Publications

The new papers were tagged with:

#

Tag

  

#

Tag

  

#

Tag

  

#

Tag

5

Cloud

3

Other

1

Shared

7

UseMain

-

HowTo

-

Project

6

Tools

22

UsePublic

3

IsGalaxy

14

RefPublic

-

UseCloud

-

Visualization

50

Methods

4

Reproducibility

8

UseLocal

14

Workbench


Galaxy Arabic Community Launched

Galaxy Arabic Speaking Community

أرشيف للقائمة البريدية جالاكسي بالعربية يحتوي على الاخبار والمناقشات والاعلانات الخاصة بمستخدمي جالاكسي من البلاد الناطقة بالعربية نرحب بانضمام أي شخص مهتم بالجلاكسي بلاتفورم
جالاكسي هي بلاتفورم لتحليل المعلومات الحيوية باستخدام أدوات برمجة أونلاين مجانا تتميز بأنها متاحة للجميع ونتائجها تتميز بالشفافية وبالقدرة على الحصول على نفس النتائج عند إجراء التحليل مرات عديدة.
السهولة : يمكن لأي شخص استخدام جالاكسي حتى لو لم تكن لديه خبرة كافية بتحليل المعلومات الحيوية
النتائج : تحصل على نفس النتائج مهما أجريت التجربة مرات عديدة وهذا يميز جالاكسي عن العديد من الأدوات الاخرى
الشفافية : يمكنك أن تشارك ما توصلت إليه مع زملائك والعالم كله ويمكنك النشر أيضا .
جالاكسي مفتوحة لكل المنظمات والسرفر الرئيسي يمكنك من إجراء تحليل على المعلومات الجينية وإيضا توجد مواد تعليمية للتدريب وأماكن العمل وخدمات النشر يمكنك استخدام جالاكسي أونلاين ويمكنك أيضا تنزيلها على الكمبيوتر الخاص بك واستخدامها


We are pleased to announce the launch of the Galaxy Arabic community. Galaxy Arabic supports and promotes Galaxy activity for the Arabic speaking community and in Arabic speaking regions of the world.

If you are interested in joining the community, please

We look forward to connecting and growing the Arabic speaking Galaxy community.

Thanks,

Abdelazeem Abdelhameed <abdelazeem_abdelhameed2015505@yahoo.com> and Dave Clements

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 80 publicly accessible Galaxy servers and five semi-public Galaxy services. Here's what happened with them in October.

New Public Galaxy Servers

Insitut Curie

Institut Curie

Institut Curie Galaxy is a general purpose genomic Galaxy server that contains tools for Ion Torrent data, many RNA-Seq tools, ncPRO-seq, RSAT, Nebula tools, copy number and LOH tools, and NGS diagnostic tools. It includes a wealth of published histories and tutorials and screencasts, and email support <galaxy.contact@curie.fr> are available.

The server is sponsored by Institut Curie and anyone can use it, once you have created a login.

Alveo

Alveo

The Alveo Galaxy server applies Galaxy to the Human Communication Science (HCS). "Alveo is a platform to support research in Human Communication. The Alveo repository holds large collections of speech, video and text data and provides an API for use by research tools. Our Galaxy server implements a number of research tools for working with speech and text data and we are exploring how best to adapt tools to this environment. Current tools allow data to be pulled from the Alveo repository and processed with various text and speech processing methods."

In-depth tutorials, extensive help pages and an Alveo support forum and FAQ are available.

You'll need to create an account to use the server. Alveo is sponsored by many organizations and universities across Australia.

APOSTL

Automated Processing of SAINT Templated Layouts

The APOSTL Galaxy Server supports Automated Processing of SAINT Templated Layouts (APOSTL). It features a freely available software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data. APOSTL utilizes Significance Analysis of INTeractome (SAINT), a popular command-line software for analyzing AP data. APOSTL can process AP results from MaxQuant, Scaffold, PeptideShaker, or any software that can export mzIdentML. Publication-quality visualizations are supported and include interactive bubble plots, protein-protein interaction networks through Cytoscape.js integration, and pathway enrichment/gene ontology plots.

See APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data, Brent M. Kuenzi, et al., J. Proteome Res., DOI: 10.1021/acs.jproteome.6b00660 and An Interactive Tool for Reproducible Analysis of Affinity Proteomics Data (presented by Paul A Stewart at GCC2016).

A Quick Start guide is available. APOSTL support is provided by the Haura and Rix labs at the Moffitt Cancer Center.

ARGs-OAP

Structured ARG reference database Online Analysis Platform

The ARGs-OAP Galaxy Server performs fast annotation and classification of antibiotic resistance gene-like sequences from metagenomic data. "SARG was curated to remove redundant sequences and optimized to facilitate query sequence identification by similarity. A database with a hierarchical structure (type-subtype-reference sequence) was then constructed to facilitate classification (assigning ARG-like sequence to type, subtype and reference sequence) of sequences identified through similarity search." The server integrates "ARDB and CARD, the two most commonly used databases into SARG DB and uses a hybrid functional gene annotation pipeline to do fast annotation and classification of ARG-like sequences from metagenomic data.

See ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database, Ying Yang et al., Bioinformatics (2016) 32 (15): 2346-2351. doi: 10.1093/bioinformatics/btw136. Source code is available on GitHub. ARGs-OAP has a manual as well.

The server is supported by the Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong; the School of Marine Sciences, Sun Yat-Sen University, Guangzhou, China, and Department of Plant, Soil, and Microbial Sciences, Michigan State University

Semi-Public Galaxy Services

Jetstream was officially launched in September and was added to the Semi-Public Galaxy Services list:

US: Galaxy on Jetstream Cloud update

https://www.nsf.gov/news/mmg/media/images/jetstream_logo_f_fe60185c-962f-4c1f-99bf-e6ec82d54c21.jpg

Galaxy release 16.07 is now available for free on the Jetstream cloud. This image contains the updated Galaxy application with a toolset that closely matches that of the public Galaxy server available at usegalaxy.org as well as a complete set of reference genomes available on that same server. Availability of the reference data was realized by enabling a connection to a (CVMFS-based) replica server that offers access to approximately 3TB of reference data (vs. ~50GB in the previous version of the image). An additional benefit of such integration is that the reference data is no longer stored on the machine image, reducing the size of that image to about 10GB, leaving more space for the analysis data. The base operating system is Ubuntu 14.04. The image was built using the cloud_setup flavor of the GalaxyKickStart Ansible playbook.

Galaxy Community Hubs

Galaxy Training Network

Galaxy Community Log Board

Galaxy Deployment Catalog

Share your training resources and experience now

Share your experience now

Describe your instance now


One new member organization joined the Galaxy Training Network and 3 resources were added to the Galaxy Training Resources directory in October:


Releases


https://pypi.python.org/pypi/planemo/

Planemo 0.34.1

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. Planemo saw two releases in October. These included Conda fixes, new mulled features, and browser and pip related changes too.

See GitHub for details.

galaxy-lib 16.10.10

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.

The October releases (8 of them!) added mulled and Conda enhancements.

Earlier Releases

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

Galaxy v16.07

GalaxyProject

The Galaxy Committers team is pleased to announce the July 2016 (v16.07) release of Galaxy.

Highlights

Shift of Galaxy tool dependencies to Conda

Galaxy admins obtained the ability to install Galaxy tool’s dependencies using the Conda package manager. This is a Beta feature and we encourage interested deployers to opt-in by modifying configuration. Documentation that explains this switch and answers FAQ is available.

Dynamic tool destinations

Our friends from Canada National Microbiology Laboratory enhanced Galaxy with feature that allows dynamic mapping of tools to destinations based on finer grained admin-specified rules. Please see the wiki. Implemented in PR #2579.

Galaxy chat

Admins can now plug in the included communication server to enable users of their instance to use real-time chat within the Galaxy interface. Please see the documentation to learn how to activate and use this feature. Implemented in PR #2515.

Github

New Galaxy repository

$ git clone -b release_16.07 https://github.com/galaxyproject/galaxy.git

Update of existing Galaxy repository

$ git checkout release_16.07 && git pull --ff-only origin release_16.07

See our wiki for additional details regarding the source code locations.


See the full release notes for more.

Galaxy Docker Image 16.07

And, thanks to Björn Grüning, there is also now a Docker image for Galaxy 16.07 as well.

CloudBridge 0.1.1

CloudBridge provides a simple layer of abstraction over different cloud providers, reducing or eliminating the need to write conditional code for each cloud. The latest release adds support for advanced networking management and OpenStack Keystone v3 support (required to use NSF Jetstream cloud).

BioBlend 0.8.0

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 0.8.0.


Pulsar

Pulsar 0.7.1 - 0.7.2

Pulsar updates were released in August. Pulsar is a Python server application that allows a Galaxy server to run jobs on remote systems (including Windows) without requiring a shared mounted file systems. Unlike traditional Galaxy job runners - input files, scripts, and config files may be transferred to the remote system, the job is executed, and the results are transferred back to the Galaxy server - eliminating the need for a shared file system.

And the rest ...

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



Galaxy ToolShed

ToolShed Contributions

Tool Shed contributions for October.

And, we are happy to announce that Lance Parsons just joined the IUC to help the Galaxy community with improved and more user-friendly tools.