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 .
Python 2.6 is no longer supported. Details: 16.01 release announcement
The Galaxy source is no longer hosted on Bitbucket. Details: 16.04 release announcement.
On behalf of the Galaxy Core and Contributor team (and community), Thanks for using Galaxy!
November 7-11, 2016
University of Utah
Salt Lake City, Utah
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.
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.
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).
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
The August Galaxy News is out:
Open positions (hurry!)
And other news too.
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 <firstname.lastname@example.org>.
Some highlights from the July Galaxy News:
GCC2016 is done! and slides and posters are now online (and video and training materials are coming)
- And there is plenty more happening:
And other news too.
Hope to see you in Montpellier!
Some highlights from the June Galaxy News
Papers (76 of them, 4 highlighted)
Open positions (5 of them)
A new Galaxy Trainer
Hope to see you in Bloomington,
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.
Please note that Python 2.6 is no longer supported as of this release. See the 16.04 release announcement for details.
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
See the Get Galaxy page for additional details regarding the source code locations.
Thanks for using Galaxy!
Some highlights from the May Galaxy News
New tutorials and video on Diploid Variant Calling, Reference Based RNA-Seq, and Dataset Collections.
Papers (72 of them, 8 highlighted)
Open positions (6 of them)
A new Galaxy Community Hub training resource
Don't miss those deadlines, and see you in June,
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.
List of tools (versions) added to Bioconda:
List of tools in [WIP]:
- All perl packages on osx
- Bioconductor minfi
List of tools removed from .tt_blacklist in IUC
Thanks to everyone who participated!
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:
- Browse the available images and choose "Galaxy 16.01 Standalone"
- Follow the prompts on the screen to launch an instance
- 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
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.
Pick a good descriptive, CamelCase page name.
- Type it in a box below and hit the "Create" button.
- See MoinMoin help
- 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.
- Save, review, and edit the page until you are happy with it.
- 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.