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News/Archive/2016

2016 News Item Archive

This page shows older news items that were posted to the Galaxy News page/feed in 2016.

See also 



 

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 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

March News

The March 2016 Galactic News is hot off the presses:

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2016-03-01

GalaxyProject

See the full release notes.

The Galaxy Committers team is pleased to announce the January 2016 (v16.01) release of Galaxy.

Galaxy administrators should also be aware of the security announcements linked to below.

Highlights

Interactive Tours

The interactive tours framework allows developers and deployers to build interactive tutorials for users superimposed on the actual Galaxy web front end. Unlike video tutorials, these will not become stale and are truly interactive (allowing users to actually navigate and interact with Galaxy). Galaxy 16.01 ships with two example tours and new ones can easily be added by creating a small YAML file describing the tour. Try the Galaxy UI tour on Main.

Wheels

Galaxy’s Python dependencies have traditionally been distributed as eggs using custom dependency management code to enable Galaxy to distribute binary dependencies (enabling quick downloads and minimal system requirements). With this release all of that infrastructure has been replaced with a modern Python infrastructure based on pip and wheels. Work done as part of this to enable binary dependencies on Linux has been included with the recently released pip 8.

Detailed documentation on these changes and their impact under a variety of Galaxy deployment scenarios can be found in the Galaxy Framework Dependencies section of the Admin documentation.

Nested Workflows

Workflows may now run other workflows as a single abstract step in the parent workflow. This allows for reusing or subworkflows in your analyses.

Github

New
% git clone -b master https://github.com/galaxyproject/galaxy.git

Update to latest stable release
% git checkout master && pull --ff-only origin master

Update to exact version
% git checkout v16.01

BitBucket

Upgrade
% hg pull
% hg update latest_16.01

See the Get Galaxy page for additional details regarding the source code locations.

Deprecation Notices

Barring a strong outcry from deployers, 16.01 will be the last release of Galaxy to support Python 2.6. For more information, see Galaxy Github Issue #1596.



Security Announcements

Read/write arbitrary filesystem paths, arbitrary code execution

Multiple security vulnerabilities were recently discovered in Galaxy that allow malicious actors to read and write files on the Galaxy server. Additionally, Galaxy servers on which a rarely used feature has been enabled are vulnerable to an arbitrary code execution exploit.

This issue affects all known releases of Galaxy in at least the last 3 years. See the full announcement for details.

Tool Shed Security Vulnerability - Read/write arbitrary filesystem paths

Multiple security vulnerabilities were recently discovered in the Tool Shed that allow malicious actors to read and write files on the Tool Shed server outside of normal Tool Shed repository directories.

This issue affects all known releases of Galaxy in at least the last 3 years. See the full announcment for details.

Posted to the Galaxy News on 2016-02-24

2016 Galaxy Community Conference

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.

Applicants are required to

  1. Either

      • Submit a poster and/or demo abstract. Or,
      • Submit a 200-250 word essay on how attending GCC2016 will benefit your research and career.
    Poster/demo abstracts are strongly preferred. The essay option should only be used by those who are starting their research careers.

  2. Have a faculty member / PI send a letter of recommendation to community-fund@lists.galaxyproject.org no later than May 10 or March 27 (depending on your deadline).

  3. Submit an application form.

  4. Have sufficient funds to cover your own travel and other expenses

If you are submitting a poster or demo, please do so before submitting an application. You also need to identify and ask a faculty member to write a letter of recommendation prior to applying.

The application deadline is May 1 for members of historically underrepresented groups and March 20 for those from Low and Lower-Middle Income Economies. Applicants will be notified of their scholarship status no later than two weeks after the deadline.

Galaxy Community Fund Board

Posted to the Galaxy News on 2016-02-18

Bioinformaticist @ Johns Hopkins APL

The Johns Hopkins University Applied Physics Laboratory (APL) is seeking a bioinformatics expert to join the Biological Sciences and Engineering Group (REDD\R1C). They are seeking someone with "demonstrated expertise in the analysis of sequencing data to contribute to innovative research in synthetic biology and infectious disease mitigation."

If you are a US citizen with Unix chops, programming experience, analysis skills, and have "Familiarity with the Galaxy platform for bioinformatic analysis, to include experience administering a local Galaxy instance" then please give them a shout.

Dave Clements

Posted to the Galaxy News on 2016-02-05

It's a new year in the Galaxy!

The February 2016 Galactic News is hot off the presses. Here are some highlights:

GCC2016 early registration and abstract submission are now open.

  • Register early and save up to 40% off regular registration costs. Early bird prices start at less than $45 / day for post-docs and students.

  • Abstract submission is open as well. If you are doing work in data-intensive biology then you are strongly encourage to present your work at the conference. Oral presentations, poster presentations, and the new Visualization Showcase & Software Demos are all opportunities to share your work.

  • And, we have two new sponsors: Please welcome Lenovo and Globus Genomics to GCC2016.

And lots of new, new, new, new:

And other cool bits too:

Happy February!

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2016-02-02

A history in Galaxy Portal

Galaxy is now accessible from your IOS and Android devices. The Galaxy Portal app is a quick and easy way to monitor the status of biomedical research on any Galaxy server. With this app you can set up a list of Galaxy connections and browse your analyses histories in a user-friendly format and take a peek at your data on the go.

The app has been in development for over a year at the University of Oslo as part of Claus Børnich's masters thesis and is described in

A user manual, additional information, and the full source are available on GitHub.

Galaxy Portal is provided free of charge.

Posted to the Galaxy News on 2016-02-02

A postdoc position in bioinformatics is available in Oslo (Norway) on development of methods for transcriptome analysis of disease-specific cells.

The postdoc will be part of a newly established research center and will work in the intersection between two environments: A research group at immunology will provide hypotheses and challenges at the forefront of research on autoimmunity, as well as a rich collection of unique data, including transcriptomic data on sharply selected populations of B cells in a disease-relevant setting. A research group at computer science has long experience with development of software systems, algorithms and statistical methodology for the analysis of genomic and epigenomic data, including an established codebase for genome analysis (the Galaxy-based Genomic HyperBrowser") that can be drawn on for future computational development.

The salary is good and there are good future career opportunities. Further details on the positions and how to apply are available in the full announcement.

Postdoc position on methods for transcriptome analysis of disease-specific cells in Oslo

Posted to the Galaxy News on 2016-02-01