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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

GalaxyProject


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


Reminders


Highlights

v16.07 Galaxy Release Highlights


Get Galaxy

v16.07 Galaxy Release Github


On behalf of the Galaxy Core and Contributor team (and community), Thanks for using Galaxy!

Posted to the Galaxy News on 2016-08-25

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

Registration is open

We are pleased to announce that registration for Galaxy Admin Training 2016 is now open.

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 as well.

Advanced Session: November 9-11

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

Register by September 19 and save up to $130 off standard registration rates (and up to $250 if you work in industry).


University of Utah Center for High Performance Computing (CHPC)   University of Utah University of Utah Department of Biomedical Informatics University of Utah Clinical & Translational Science Biomedical Informatics Core (CCTS BMIC)

Galaxy Admin Training 2016 is hosted by the University of Utah Center for High Performance Computing (CHPC), the Department of Biomedical Informatics and the Clinical & Translational Science Biomedical Informatics Core (CCTS BMIC) at the University of Utah.

We hope to see you in Salt Lake!

The Galaxy Team

Posted to the Galaxy News on 2016-08-23

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

Want More?

See the News Archive for older postings.


Add a News Item

News items on this page have a very specific format that allows an RSS feed generator to parse the page and create an RSS feed. Each item is created using the News Template, which provides you with a page skeleton that has the needed format.

  1. Pick a good descriptive, CamelCase page name.

  2. Type it in a box below and hit the "Create" button.
  3. Follow the instructions on that page: set the page title (35 chars or less, including spaces) and populate the new page with your news item text. Try to keep it short.
  4. Save, review, and edit the page until you are happy with it.
  5. Return to this page, and add a link at the top of the News Items section using the include macro. This final step will publish your item to this page and to the RSS feed. For example, if your news item page is "My News Item", add this:
    • <<Include(New/MyNewsItemPageName, , to="^CategoryNews")>>

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.