April 2016 Galaxy News

Galaxy News

Welcome to the April 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

2016 Galaxy Community Conference

GCC2016 will be held June 25-29 at Indiana University in Bloomington, Indiana, United States. This will be the 7th annual gathering of the Galaxy community, and we are expecting over 200 participants again this year. The 2016 Galaxy Community Conference includes 2 days of hackathons, 2 days of training, and a two day meeting featuring accepted presentations, keynotes, poster sessions, the new Visualization Showcase and Software Demo sessions, lightning talks, birds-of-a-feather meetups, and plenty of networking.

GCC2016 Abstract Deadline extended to April 8!

   Submit an abstract   

The deadline for oral presentation abstracts has been extended to April 8, 2016. Abstracts will be reviewed and submitters will be notified of acceptance status no later than April 22, 2016.

Poster and Demo abstract submission closes May 20, 2016 (or earlier depending on poster space availability). Poster and demo submissions are reviewed on a rolling basis, and submitters will be notified of acceptance status no later than two weeks after the abstract is submitted. You may submit similar content for oral presentations, posters, and demos.

Topics should be of interest to those working in high-throughput data analysis and research. Presentations that are Galaxy-centric are encouraged, but not required. Please see the abstracts page for full details.

GCC2016 Early Registration

   Register Now   

Early registration for GCC2016 is now open. Registration costs depend on which events you register for, your career stage & affiliation, and when you register. Early bird registration ends May 20 and is up to 40% less than regular registration rates. Early bird registration starts at less than $45 / day for students and postdocs, and at $65 / day for other attendees from non-profits.

You can also sign up for conference housing during registration.

You are strongly encouraged to review the training and housing options before beginning the registration process.

Scholarships: Application deadline is May 1

Scholarships: Apply now

We are pleased to offer scholarships for the 2016 Galaxy Community Conference, being held in Bloomington, Indiana, United States, June 25-29. Scholarships are available to students and post-docs in historically under-represented groups, and to those from or based in Low and Lower-Middle Income Economies, as defined by the World Bank. If this describes you or one of your students then we hope to receive an application.

Scholarships cover registration and lodging during the GCC Meeting, and for any Training or Hackathon events the applicant chooses to attend. Scholarships do not cover travel or other expenses. The application deadline is May 1 for members of historically underrepresented groups.

See the full announcement for details.

Sponsors

BioTeam

Please welcome the Indiana Health Industry Forum (IHIF) as a new GCC2016 Sponsor. IHIF is a statewide trade association representing members of Indiana's health science business community. Our mission is to connect key stakeholders to: enhance business networks, advocate for member interests, develop workforce skills, and provide strategic vision in the interest of growing the state’s health industry economy and reputation.

We continue to seek other sponsors as well and offer a wide range of sponsorship plans. If your organization is interested in having a presence at GCC2016, please contact the GCC2016 Exec for more information.


Events

Galaxy DevOps Workshop - Heidelberg, 6-7 April

We would like to invite you to our Galaxy DevOps Workshop in Heidelberg from 6-7 of April, organised by de.NBI and ELIXIR.

The workshop is intended for Bioinformaticians who want to

Galaxy DevOps Workshop - Galaxy and Galaxy tools deployment strategies

Galaxy DevOps Workshop - Galaxy and Galaxy tools deployment strategies

Galaxy DevOps Workshop - Galaxy and Galaxy tools deployment strategies
  • learn the internals of the multi-omics Galaxy workbench
  • learn how to set up and run a Galaxy server
  • learn about Galaxy tool development
  • get questions answered from experienced Galaxy admins and community members
  • are interested in reproducible and accessible research

The workshop will be held at Heidelberg Center for Human Bioinformatics (HD-HuB). Location and Accommodation options can be found here.

Registration is open and their is still space - just send Björn Grüning an email. For more information please see the workshop page.


IFB
Institut Pasteur
Technical Hackathon : Tools, Workflows and Workbenches

Hackathon: Tools, Workflows and Workbenches, 18-20 May

A hackathon bringing together developers from the ELIXIR Tools & Data Services Registry, Galaxy, Taverna, Arvados, CWL, ReGaTE and EDAM ontology, with Galaxy instance providers from ELIXIR and beyond, to promote collaboration and technical developments will take place on 18-20 May 2016 at the Institut Pasteur in Paris.

Registration is free but space is limited.

Report: IUC Contribution Fest - RADSeq Tools and Workflows

remote Contribution Fest was held 7th and 8th of March for developers to work on Galaxy RADSeq tools

A remote Contribution Fest was held 7th and 8th of March for developers to work on Galaxy RADSeq tools. RADSeq is a cheap sequencing technology that is used by many resource-limited groups who would benefit a lot from easy-to-use galaxy tools. Indeed there has been quite some interest in analyzing RADSeq with Galaxy. Currently there is a wrapper for stacks and little more to help with RAD specific analysis (though many other galaxy tools are useful with RADs - bwa, cap3, gatk, velvet, ...).

A hackathon report page is available on the GenOuest GUGGO wiki.

Upcoming Events

There are many upcoming events in the next few months. See the Galaxy Events Google Calendar for details on other events of interest to the community.

Galaxy DevOps Workshop - Galaxy and Galaxy tools deployment strategies   21 April GalaxyAdmins Web Meetup   Workshop on Galaxy: Practical Course   NGS Bioinformatics Data Analysis Workshop Galaxy Workshop Tokyo 2016
Date Topic/Event Venue/Location Contact
April 6 Approaches for the Integration of Visual and Computational Analysis of Biomedical Data North America BioIT World 2016, Boston, Massachusetts, United States Nils Gehlenborg
April 6-7 Galaxy DevOps Workshop - Galaxy and Galaxy tools deployment strategies Europe Galaxy DevOps Workshop 2016, Heidelberg, Germany Training offered by GTN Member Björn Grüning
April 21 GalaxyAdmins Web Meetup Around the World Online Hans-Rudolf Hotz, Dave Clements
April 22-26 Workshop on Galaxy: Practical Course North America SolBio International Conference 2016, Riviera Maya, México Oswaldo Trelles
April 26 NGS Bioinformatics Data Analysis Workshop Europe NGS 2016 Glasgow, Glasgow, United Kingdom Julian Augley, Graham Hamilton, David Meltzer, Mani Mudaliar
April 28 Galaxy Workshop Tokyo 2016 Asia RCAST, The University of Tokyo, Japan Tazro Ohta, James Taylor
May 11-13 NGS & Cancer : Analyses RNA-Seq Europe Paris, France Cancéropôle Île-de-France
May 18-20 ELIXIR Technical Hackathon: Tools, Workflows and Workbenches Europe Institut Pasteur, Paris, France Organisers
May 23-24 Analyse statistique de données RNA-Seq sous Galaxy -Recherche des régions d'intérêt différentiellement exprimées Europe Part of Le cycle "Bioinformatique par la pratique" 2016, Jouy-en-Josas, France Formation Migale
May 30 Initiation à l’utilisation de Galaxy Europe Part of Le cycle "Bioinformatique par la pratique" 2016, Jouy-en-Josas, France Formation Migale
May 31 Analyse primaire de données issues de séquenceurs nouvelle génération sous Galaxy Europe Part of Le cycle "Bioinformatique par la pratique" 2016, Jouy-en-Josas, France Formation Migale
June 9-10 Informatics on High-throughput Sequencing Data North America Montreal, Quebec, Canada Training offered by GTN Member Francis Ouellette
June 13-17 Using Galaxy For Analysis of High Throughput Sequence Data North America Davis, California, United States Training offered by GTN Member UC Davis Bioinformatics Training Program
June 25-29 2016 Galaxy Community Conference (GCC2016) North America Indiana University, Bloomington, Indiana, United States Training offered by GTN Member Organizers
June 30 - July 1 GMOD Meeting North America Indiana University, Bloomington, Indiana, United States Scott Cain
Designates a training event offered by GTN Member Designates a training event offered by GTN member(s)

New Papers

86 new papers referencing, using, extending, and implementing Galaxy were added to the Galaxy CiteULike Group in March.

It was a banner month for Galaxy-related papers. Some of the highlights:

The new papers were tagged with:

# Tag    # Tag    # Tag    # Tag
- Cloud 6 Other 3 Shared 14 UseMain
3 HowTo - Project 5 Tools 17 UsePublic
5 IsGalaxy 9 RefPublic - UseCloud - Visualization
44 Methods 4 Reproducibility 4 UseLocal 17 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

1 new publicly accessible Galaxy server was listed in March:

Halogen Bonding

Halogen Bonding Webserver

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


Two new Community Log entries were added in March

As were two and two new training organizations.


Releases


Planemo 0.24.0

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. Planemo 0.24.0, the most recent release, features these updates:

See the release history.

CloudMan 16.03

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.

Most notable changes include:

  • Galaxy 16.01 release
  • A fine-grained control over auto-scaling options
  • Several fixes to cluster sharing and cloning

See the CHANGELOG for a more complete set of changes.

Earlier Releases

Galaxy v16.01

GalaxyProject

The January 2016 (v16.01) release of Galaxy features

  • Interactive Tours
  • Wheels
  • Nested Workflows

See the announcement for full details.

Galaxy Docker Image 16.01

And, thanks to Björn Grüning, there is also now a Docker image for Galaxy 16.01 as well.

galaxy-lib 16.4.0

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.

CloudBridge 0.1.0

The Galaxy Team is proud to be part of the development team for a new cross-cloud library called CloudBridge. CloudBridge is a Python library providing a simple layer of abstraction over different cloud providers, reducing or eliminating the need to write conditional code for each cloud. The library is generally applicable to any domain wishing to run cloud-independent applications. There is already support for Amazon and OpenStack clouds with support for Google’s Compute Engine in development.

The first version of CloudBridge was released earlier this month and it comes with detailed user documentation. The source code is available on Github.

Starforge 0.1

Starforge

Starforge is a collection of scripts that supports the building of components for Galaxy. Specifically, with Starforge you can:

These things will be built in Docker. Additionally, wheels can be built in QEMU/KVM virtualized systems.

Documentation can be found at starforge.readthedocs.org.


Pulsar

Pulsar 0.6.1

Pulsar 0.6 was released in December. 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.

The 0.6.x release includes these changes:

  • Pulsar now depends on the new galaxy-lib Python package instead of manually synchronizing Python files across Pulsar and Galaxy.
  • Numerous build and testing improvements.
  • Fixed a documentation bug in the code (thanks to @erasche). e8814ae
  • Remove galaxy.eggs stuff from Pulsar client (thanks to @natefoo). 00197f2
  • Add new logo to README (thanks to @martenson). abbba40
  • Implement an optional awknowledgement system on top of the message queue system (thanks to @natefoo). Pull Request 82 431088c
  • Documentation fixes thanks to @remimarenco. Pull Request 78, Pull Request 80
  • Fix project script bug introduced this cycle (thanks to @nsoranzo). 140a069
  • Fix config.py on Windows (thanks to @ssorgatem). Pull Request 84
  • Add a job manager for XSEDE jobs (thanks to @natefoo). 1017bc5
  • Fix pip dependency installation (thanks to @afgane) Pull Request 73

BioBlend 0.7.0

BioBlend version 0.7.0 was released at the beginning of November. BioBlend is a python library for interacting with CloudMan and the Galaxy API. 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.) From the release CHANGELOG.

blend4j v0.1.2 blend4j v0.1.2 was released in December 2014. blend4j is a JVM partial reimplemenation of the Python library bioblend for interacting with Galaxy, CloudMan, and BioCloudCentral.



Galaxy ToolShed

ToolShed Contributions

See list of tools contributed in March.

Automatic Testing of IUC Tools with Conda

Conda

An effort is underway to test more and more IUC tools automatically using Conda dependencies. The final aim of getting all tools under test by simply installing the dependencies via conda before running planemo test. Getting packages in Conda also means we can automatically build Docker containers and offer Docker and Conda dependency resolutions for everyone today and for testing.

The IUC is seeking comments and contributions to this effort.


Other News

New and updated tools on usegalaxy.org