July 2016 Galaxy News

Galaxy News

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

If you have anything to include in the next News, please send it to Galaxy Outreach.

GCC2016 is done!

2016 Galaxy Community Conference

And it was again a smashing success! For the 5th year in a row we had over 200 participants signed up for GCC events, including hackathons, training, and the two day meeting. The meeting featured accepted presentations and keynotes, posters, the new Visualization Showcase and Software Demo sessions, lightning talks, and birds-of-a-feather meetups.

GCC2016 was held June 25-29 at Indiana University in Bloomington, Indiana, United States. This was the 7th annual gathering of the Galaxy community.

Slides for accepted and lightning talks are online, as are most posters. Remaining slides and video of training and talks will also be posted online this month.

Thanks to everyone for making GCC2016 a success, and looking forward to seeing you at GCC2017!

Upcoming Events

Several upcoming events were announced / highlighted at GCC2016:

GCC2017: 26-30 June 2017, Montpellier, France

2017 Galaxy Community Conference (GCC2017)

GCC returns to Europe in 2017!

The 2017 Galaxy Community Conference (GCC2017) will be held 26-30 June in Montpellier, France. Montpellier is home to three universities, and is the agronomy hotspot in France. The city is home to half a million people is the third largest city of France's Mediterranean coast.

GCC2017 will feature hackathons, two days of training and a two day meeting highlighting the best that data intensive biology has to offer.

All conference events will be at the Le Corum Conference Center, located in central Montpellier, next to the train station, and a 15 minute ride from the Montpellier International Airport. GCC2017 is hosted by the French Institute of Bioinformatics (IFB).


2016 Swiss German Galaxy Tour

Swiss-German Galaxy Days

There will be a Swiss-German Galaxy Tour this fall featuring a range of events over 2 days in October. Events will held in Freiburg (Germany).

Registration is free, but space is limited on both days. We recommend you register soon to secure your spot for one or both days of the SG2016Tour: Register Now

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

The first ever Galaxy Project Admin Training workshop will be held November 7-11 in Salt Lake City Utah. The workshop features a 2 day basics session followed by a 3 day advanced session. There is a separate registration for each session, and participants may sign up for one or both. We are working with the Utah High Performance Computing Center at the University of Utah for cluster access during the advanced session.

The introductory session will be at the Salt Lake City Library, and the advanced session will be on the University of Utah (the "U") campus. Workshop housing is on the U as well.

The curriculum will be published and registration will open later this month. Watch this space. This workshop is the week before Supercomputing'16 meets in Salt Lake.

European Galaxy Developer Knowledge Exchange

ELIXIR

ELIXIR, the European life-science Infrastructure for Biological Information, aims to orchestrate the collection, quality control, share-ability and archiving of large amounts of biological data produced by life science experiments and the resources to compute with this data.

Galaxy is widely used in the ELIXIR community. The French ELIXIR node (IFB) and the ELIXIR Galaxy Working Group will organize a knowledge exchange workshop in January 2017 (date tbc) in Strasbourg (France). This workshop will be for developers that want to set up a Galaxy instance, wrap tools and use Galaxy for data analysis and visualisation.

Galaxy AustralAsia Meeting (GAMe 2017), 3-9 February, Melbourne

Galaxy Australasia Meeting (GAMe 2017)

The Galaxy Australasia Meeting (GAMe 2017) will be held 3-9 February in Melbourne Australia. The schedule has been set:

3 February Using Galaxy Training
Morning and afternoon sessions covering 4 topics in two parallel tracks 4-5 February Meeting
A two day meeting of the Galaxy AustralAsian communities featuring accepted and invited talks, posters and panel discussions on best practices, data intensive research, and the computational infrastructure to support it. 6-9 February Admin Training
Four days of intense hands-on training on Galaxy Administration, based on the Galaxy Admin Training offered in the US in November.

Instructors and speakers will include experts from Australia and Asia, as well as members of the Galaxy Team. Training sessions and instructors will be announced shortly. Registration and abstract submission will open in August. Watch this space.

Other upcoming events

There are a plentitude of Galaxy related events coming up. Here's what's coming up over the next fe months:

BOSC 2015 ISMB 2016 An Introduction to Using Galaxy for Genetic Data Analysis @ TAGC
Date Topic/Event Venue/Location Contact
July 4-8 An introduction to Galaxy with the NeCTAR Genomics Virtual Laboratory Workshop Australia 2016 Winter School in Mathematical & Computational Biology, University of Queensland, Brisbane, Australia Igor Makunin, Derek Benson
July 6-7 BOSC Codefest 2016 North America Orlando, Florida, United States Brad Chapman
July 8-9 BOSC 2016 North America ISMB 2016, Orlando, Florida, United States See presenters
July 8-12 ISMB 2016 North America Orlando, Florida, United States See presenters
July 13-17 An Introduction to Using Galaxy for Genetic Data Analysis North America The Allied Genetics Conference 2016 (TAGC), Orlando, Florida, United States Dave Clements
July 15 Introduction to Galaxy Workshop
This workshop is full
Europe University of Glasgow, Glasgow, United Kingdom David Meltzer
July 19-20 Introduction to Galaxy North America University of Rochester, Rochester, New York, United States Training offered by GTN Member Dave Clements
July 21 Introduction to Galaxy North America Cornell University, Ithaca, New York, United States Training offered by GTN Member Dave Clements
August 1-4 Integrating Ontological and Genomic Analysis with Galaxy Workshop North America ICBO 2016, Corvallis, Oregon, United States Training offered by GTN Member Dave Clements
August 9-10 Introduction to Galaxy Workflows Around the World Workflows Workshop, Distributed Training offered by GTN Member Dave Clements
August 12 Introduction to Galaxy Workshop Europe University of Glasgow, Glasgow, United Kingdom David Meltzer
August 18 GalaxyAdmins Web Meetup Around the World Online Hans-Rudolf Hotz, Dave Clements
August 29 - September 2 Using Galaxy for Analysis of RNA-Seq, Exome-Seq, and Variants North America Davis, California, United States Training offered by GTN Member UC Davis Bioinformatics Training Program
September 3-7 Tutorial: Scientific workflows under Galaxy. Use case: multiple genome comparison Europe European Conference on Computational Biology (ECCB 2016), The Hague, Netherlands Oswaldo Trelles Salazar
September 12-16 Summer School 2016 in Metagenomics Europe Institut Pasteur, Paris, France Contacts
September 19-23 High Throughput Sequencing (HTS) Data Analyses for Scientists
This workshop is full
Europe Freiburg, Germany Training offered by GTN Member Contact
October 18-20 Galaxy4Bioinformatics Europe Lyon, France Training offered by GTN Member Contacts
October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany Hans-Rudolf Hotz and Bjoern Gruening
October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany Hans-Rudolf Hotz and Bjoern Gruening
November 7-8 Galaxy Admin Training: Introduction North America Salt Lake City, Utah, United States Training offered by GTN Member Galaxy Team
November 9-11 Galaxy Admin Training: Advanced North America Salt Lake City, Utah, United States Training offered by GTN Member Galaxy Team
2017
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
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 Papers

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

Some highlights from last month:

Tagged Publications

The new papers were tagged with:

# Tag    # Tag    # Tag    # Tag
3 Cloud 1 Other 1 Shared 15 UseMain
- HowTo - Project 3 Tools 14 UsePublic
4 IsGalaxy 6 RefPublic - UseCloud - Visualization
47 Methods 5 Reproducibility 6 UseLocal 22 Workbench

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.



New Public Galaxy Servers

One new publicly accessible Galaxy servers was added to the list in June:

Chemical Annotation Retrieval Toolkit (CART)

Chemical Annotation Retrieval Toolkit (CART) Galaxy
  • Link:
  • Domain/Purpose:
    • Retrieves annotations on biological effects of chemicals and determines which ones are enriched.
  • Comments:
    • From "CART – a chemical annotation retrieval toolkit" by Samy Deghou, Georg Zeller, Murat Iskar, Marja Driessen, Mercedes Castillo, Vera van Noort, and Peer Bork. Bioinformatics (2016), doi: 10.1093/bioinformatics/btw233 "it matches an input list of chemical names into a comprehensive reference space to assign unambiguous chemical identifiers. In this unified space, bioactivity annotations can be easily retrieved from databases covering a wide variety of chemical effects on biological systems. Subsequently, CART can determine annotations enriched in the input set of chemicals and display these in tabular format and interactive network visualizations, thereby facilitating integrative analysis of chemical bioactivity data."
    • Source code and an easy-to-install command line tool are also available.
  • User Support:
    • See the "Tutorial" and "Contact" tabs on the website.
  • Quotas:
    • Supports anonymous access and creation of user logins.
  • Sponsor(s):

New Semi-Public Galaxy Servers

And one new set of Semi-Public Galaxy server was added in June. Semi-public servers aren't fully publicly accessible, but that are accessible to a larger group than just the host institution's members.

Norway: NeLS

NeLS Portal

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 community log board entry was added:


Releases

blend4php 0.1 alpha

We are pleased to announce the alpha release of the blend4php package, a PHP wrapper for the Galaxy API. It follows the lead of BioBlend which provides a Python package for interacting with Galaxy and CloudMan--hence the use of 'blend' in the name of this package. blend4php currently offers a partial implementation of the Galaxy API and includes support for datasets, data types, folder contents, folders, genomes, group roles, groups, group users, histories, history contents, jobs, libraries, library contents, requests, roles, search, tools, toolshed repositories, users, visualizations and workflows.

The motivation for development of this library is for integration with Tripal, an open-source toolkit for creation of online genomic, genetic and biological databases. Integration of Tripal and Galaxy will allow the community research databases to provide next-generation analytical tools to their users using Galaxy. However, this library was created independently of Tripal to support integration of any PHP application with Galaxy.

Please see the API documentation page for full information.


Planemo 0.27.0

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. Planemo 0.27.0 was released in June. Some highlights:

See the release history.

galaxy-lib 16.7.8 - 16.7.9

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.

Highlights of June releases include:

  • Updates for recent changes to Galaxy and cwltool.
  • Updates to include Galaxy library for verifying test outputs and the latest dev changes to Galaxy.

Earlier Releases

Galaxy v16.04

GalaxyProject

The Galaxy Committers team is pleased to announce the April 2016 (v16.04) release of Galaxy.

Please note that Python 2.6 is no longer supported as of this release. See the 16.04 release announcement for details.

Highlights

Tool Profile Versions

Tools may now declare which version of Galaxy they require. Tools requiring 16.04 or newer will have new default behaviors (such as using exit code for error detection) that should simplify tool development. See PR #1688.

Embedded Pulsar Job Runner

Galaxy can now start a Pulsar application embedded within the Galaxy process itself. This allows using Pulsar’s job staging and isolation without requiring a RESTful web service or a message queue. This is enabling usegalaxy.org to run jobs to on the new JetStream cloud. See PR #2057.

New Chemical Datatypes

Galaxy now detects and supports many molecular datatypes. See PR 1941. Thanks to Björn Grüning (@bgruening).

Github

New
% git clone -b master https://github.com/galaxyproject/galaxy.git

Update to latest stable release
% git checkout master && git pull --ff-only origin master

Update to exact version
% git checkout v16.04
BitBucket

Upgrade
% hg pull
% hg update latest_16.04
See the Get Galaxy page for additional details regarding the source code locations.
Galaxy Docker Image 16.04

And, thanks to Björn Grüning, there is also now a Docker image for Galaxy 16.04 as well.

CloudMan 16.04

CloudMan

We just released an update to Galaxy CloudMan on AWS. CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration or imposed quotas. Once running, you have complete control over Galaxy, including the ability to install new tools.

This is a minor update release with the following changes:

  • Galaxy 16.04 update
  • Availability on Amazon's Ireland region
  • A couple of bug fixes

See the CHANGELOG for a more complete set of changes.


Pulsar

Pulsar 0.7.0

Pulsar 0.7 was released in April. 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

Did not get there this month. Look for a double edition next month.

Other News