August 2016 Galaxy News

Galaxy News

Welcome to the August 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.

Events

GCC2016 presentations and training are online

2016 Galaxy Community Conference

Slides for accepted and lightning talks are online, as are the posters. They have also been posted to the new F1000Research Galaxy Channel. Video of training and talks will also be posted online in the coming month.

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

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 shortly. Watch this space. This workshop is the week before Supercomputing'16 meets in Salt Lake.

Other upcoming events

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

Integrating Ontological and Genomic Analysis with Galaxy Workshop @ ICBO    Introduction to Galaxy Workshop     GalaxyAdmins Using Galaxy for Analysis of RNA-Seq, Exome-Seq, and Variants
Date Topic/Event Venue/Location Contact
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 17 Galaxy Workshop Australia St Lucia campus, University of Queensland, Australia Igor Makunin
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 The Workflow4Metabolomics (W4M) online infrastructure for omics analysis with Galaxy Europe Metabolomics Sardinian Scientific School: How to bridge metabolomics and genomics, Pula, Italy E Thévenot
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
September 26-28 NGS Course: RNA-seq data analysis Europe Leiden University Medical Center, The Netherlands Training offered by GTN Member Peter-Bram ‘t Hoen, Jan Oosting, Celia van Gelder
October 10-13 Metagenomic: amplicon analysis Europe INRA Auzeville, Auzeville, France Training offered by GTN Member Sarah Maman
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.



F1000Research Galaxy Channel

F1000Research Galaxy Channel

We are pleased to announce the new F1000Research Galaxy Channel. This channel brings together in one place presentations and posters about the Galaxy framework, including presentations from Galaxy events such as the just finished GCC2016. If you have presented Galaxy related material at a conference in either talk or poster format, please consider submitting your presentation to the Galaxy channel.

New Papers

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

Some highlights from last month:

Tagged Publications

The new papers were tagged with:

# Tag    # Tag    # Tag    # Tag
1 Cloud 1 Other - Shared 7 UseMain
1 HowTo - Project 2 Tools 10 UsePublic
1 IsGalaxy 8 RefPublic 1 UseCloud 2 Visualization
35 Methods 1 Reproducibility 5 UseLocal 6 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.



Public Galaxy Server News

There are over 80 publicly accessible Galaxy servers and four semi-public Galaxy services. Here's what happened with them in July.

Galaxy-P

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


Public Health Agency of Canada - National Microbiology Laboratory

New Galaxy Deployment Catalog and Community Log Board entries were added:


Releases

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.

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.

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

Tool Shed contributions for June and July.

Other News