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Galaxy News

This page contains announcements of interest to the Galaxy Community. These can include items from the Galaxy Team or the Galaxy community and can address anything that is of wide interest to the community.

The Galaxy News is also available as an RSS feed http://feed43.com/galaxynews.xml.

See Add a News Item below for how to get an item on this page and the RSS feed. Older news items are available in the Galaxy News Archive.

See also


News Items

Galaxy-P

University of Minnesota

A post-doctoral position is available at the University of Minnesota for development of bioinformatics tools, with a focus on applications that integrate data across ‘omics’ domains (genomics, transcriptomics, proteomics and metabolomics). A particular emphasis is in the integration of mass spectrometry (MS)-based proteomics data with other types of ‘omics’ data for applications in proteogenomics and metaproteomics. The researcher will join a successful team of developers, collaborators and users who have developed the Galaxy for proteomics (Galaxy-P) platform (see usegalaxyp.org and references).

A Ph.D. in bioinformatics, computer science, analytical chemistry or closely related field is required. Experience with MS-based proteomics data analysis is highly preferred, and familiarity with the Galaxy framework is a plus.

Interested applicants can apply directly to Dr. Tim Griffin <tgriffin@umn.edu>.

Posted to the Galaxy News on 2016-07-22

GCC2017 Announced
2016 Swiss German Galaxy Tour
ELIXIR
Galaxy News

Galaxy Project Admin Training
Galaxy Australasia Meeting (GAMe 2017)

Some highlights from the July Galaxy News:

Hope to see you in Montpellier!

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2016-07-06

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.

Posted to the Galaxy News on 2016-05-25

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.


Thanks for using Galaxy!


Posted to the Galaxy News on 2016-05-18

The codefest started via hangouts at 10am EDT on Monday April 4, with around 8 participants. It was designed to be beginner friendly, which increased contribution from the community. 4 members of the galaxy community were added as contributors to the bioconda-recipe repository as a result of this hackathon.

The codefest started with Björn Grüning giving a small introduction to Conda and its channel Bioconda. Followed by how to create a new Conda recipe and the scripts involved in it. Members of the hack started by then picking up a simple tool and creating a Pull request against both the Tools-IUC and bioconda-recipes repositories on GitHub.

The main aim of the codefest was to get community members familiar with the Conda-Galaxy integration, and to remove tools from testing blacklist (shown below).

More details are here.

Conda Dependencies Codefest

List of tools (versions) added to Bioconda:

  1. Seqtk r-75
  2. Shaker
  3. EDirect

  4. PeptideShaker and SearchGUI

  5. OpenBabel

  6. BamHash

  7. Trf

List of tools in [WIP]:

  1. All perl packages on osx
  2. Bioconductor minfi

List of tools removed from .tt_blacklist in IUC

  1. Seqtk

  2. Vegan

  3. Art

  4. Macs2

Infrastructure:

  1. Automatic push from tested tools to the Test Tool Shed in tools-iuc and bgruenings galaxytools

  2. More strict dependency handling in Bioconda

Thanks to everyone who participated!

Rémi Marenco. Nitesh Turaga, and Björn Grüning

Posted to the Galaxy News on 2016-04-07

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

Want your own Galaxy server, for free? You can now easily create Galaxy servers on the new NSF Jetstream cloud. Each server comes preconfigured with hundreds of tools and commonly used reference datasets. It only takes a couple of minutes to start one. Once running, you can use it or change it up any way you like.

How do I get access?

You must be a US-based academic to access Jetstream cloud. Access is free but it is necessary to have an XSEDE account (go to https://www.xsede.org/ to sign up) and have an active resource allocation. Getting the resource allocation is matter of writing a summary of your research in less than 100 words and waiting ~24 hrs for the application to get approved. Go to http://jetstream-cloud.org/allocations.php → "Submit and manage allocation requests" to get started; choose Startup type of allocation.

How do I launch my own Galaxy server?

After you have your XSEDE account and an active allocation:

  1. Visit https://use.jetstream-cloud.org/

  2. Browse the available images and choose "Galaxy 16.01 Standalone"
  3. Follow the prompts on the screen to launch an instance
  4. In less than 5 minutes, you should have your own, fully configured Galaxy server

More documentation about the process can be found on Galaxy’s wiki: https://wiki.galaxyproject.org/Cloud/Jetstream

Posted to the Galaxy News on 2016-04-07

Galaxy News

GCC2016 News
Two ELIXIR Sponsored Events: Galaxy DevOps Workshop - Galaxy and Galaxy tools deployment strategies; Hackathon: Tools, Workflows and Workbenches

Planemo release
CloudMan

Automatic Testing of IUC Tools with Conda

The April Galaxy News brings more than the usual amount of News of the Galaxy.

First, there are a plethora of events coming up around the world:

And a lot of new

And some other news too.

Happy April,

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2016-03-31

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.

Posted to the Galaxy News on 2016-03-24

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

For more information please see the workshop page.

Björn Grüning

Posted to the Galaxy News on 2016-03-17

Want More?

See the News Archive for older postings.


Add a News Item

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If this seems a little daunting, or you just don't want to mess with the wiki, send your news item to Galaxy Outreach and we'll post it for you.