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2014 News Item Archive

This page shows news items that were posted to the Galaxy News page/feed in 2014.

See also 


GCC2015 Training Day

GCC2015 Training Day topics are nominated by you, the Galaxy Community. Please take a few minutes to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see what topics were nominated in 2013 and 2014, and the Events and the Events Archives.

Nominated topics will be published on the Training Day page as they come in. Nominations close 6 January. Topics will be compiled into a uniform list by the GCC2015 Organising Committee, and topics will be voted on by the Galaxy Community 12-23 January.

Topics will then be selected and scheduled based on topic interest, and the organisers' ability to confirm instructors for each session.  Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens.

GCC2015 Organising Committee

Posted to the Galaxy News on 2014-12-09

Systems Administrator / Information Technologist

The McArthur Lab in the McMaster University Department of Biochemistry & Biomedical Sciences is seeking a Systems Administrator / Information Technologist to help establish a new bioinformatics laboratory at McMaster, plus develop the next generation of the Comprehensive Antibiotic Resistance Database (CARD).

From the job announcement on EvolDir:

  • The candidate will configure BLADE and other hardware for general bioinformatics analysis, development of a GIT version control system, construction of an in house Galaxy server (usegalaxy.org), and development of a new interface, stand-alone tools, APIs, and algorithms for the CARD (based on Chado).

See the full announcement for details.

Posted to the Galaxy News on 2014-12-05

Galaxy Updates

As always there's a lot going on in the Galaxy this month. "Like what?" you say. Well, read the dang December Galaxy Newsletter we say! Highlights include:

Dave Clements and the crisp Galaxy Team

Posted to the Galaxy News on 2014-12-01

Max Planck Institute of Immunobiology and Epigenetics

Max Planck Institute of Immunobiology and Epigenetics in Freiburg, Germany has an opening for a Bioinformatician for an initial period of two years. The successful candidate will work at the interface between an in-house deep-sequencing facility (HiSeq-2500) and the various research groups at the institute. Main responsibilities include

  • primary analysis of deep-sequencing data and quality controls
  • maintenance and extension of existing analysis pipelines
  • data and software management for the Bioinformatics Group
  • training and consulting

Most of the above tasks are executed within the context of our Galaxy platform that will have to be administrated and further developed. There will be ample opportunities for direct collaborations with research groups and methodological developments.

See the full job posting for further details.

Bioinformatics Uni-Freiburg

The Bioinformatics group in Freiburg, Germany recruiting creative and motivated PhD students, postdoctoral scholars or software engineers with a strong interest in RNA and NGS related bioinformatics. PhD students will work in one of our research projects and get an insight into RNA-Bioinformatics and NGS, while postdocs will have the opportunity to furthermore define their own research agenda.

Our lab has two main research areas:

  • The Galaxy project, which is an open, web-based platform to support computational biomedical research. We are integrating new tools as well as interactive visualizations into Galaxy and working closely together with Galaxy community. Besides our strong NGS focus we are also driving the development of a cheminformatic Galaxy workbench. This project is highly community- and cooperation driven, with partners from industry and academic.
  • RNA research, which includes local sequence-structure and multiple alignment of RNA, RNA folding, energy landscapes for RNA and also protein design and protein-protein Interactions.

Candidates should have a background in one or more of the following areas: genomics, computer science, visualization, or bioinformatics. A strong interest in programming and software development is as crucial as being passioned to solve scientific problems. Our lab is located in Freiburg, a beautiful university city in the south west of Germany with the Black Forest, France and Switzerland just around the corner and excellent research facilities all over the city.

Please contact Bjoern Gruening for further details.

Posted to the Galaxy News on 2014-10-30, updated on 2014-11-25

Galaxy Updates

A lot is happening in in the Galaxy in November, and a lot of good stuff happened in October too. Take a look at the November 2014 Galaxy Newsletter for the complete story, but here are some highlights:

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2014-11-03

Galaxy User Group Grand Ouest (GUGGO)

Three events were sponsored by the Galaxy User Group Grand Ouest (GUGGO) in western France earlier this fall. Summaries of all 3 events are now available online.

The Tools integration on Galaxy Workshop was held 11 September. The summary includes several of the talks (click on "Supporting Docs"). The Fourth GUGGO meeting followed on 15 September. A meeting summary and report are available. Finally, the RADseq analysis using STACKS on Galaxy Workshop was held on 25 September. Supporting docs (Galaxy tutorial as original Julian Catchen & William Cresko STACKS support) are reachable here.

And many more GUGGO resources are available online as well.

Merci to all who attended and contributed to the success of these events,

Yvan Le Bras

Cyril Monjeaud

Olivier Collin

Posted to the Galaxy News on 2014-10-31

Swiss-German Galaxy Tour 2014

After the big success of the first Swiss Galaxy Workshop two years ago, we decided to organize a similar event again this fall. This time, we added a training day prior to the workshop, and a developer day after the workshop. The first two days were held in Bern (Switzerland), and the third in Freiburg (Germany). Hence we called the whole event: "Swiss German Galaxy Tour 2014".

More than 40 people registered for the event, signing up for one, two or all three days, depending on their interest and familiarity with Galaxy. It was great to see, and we attracted participants from all over Europe (not just Germany and Switzerland). On the training day, we promoted Galaxy by offering several hands-on sessions covering diverse topics such as the simple use of Galaxy, NGS analysis, and installing your own Galaxy instance in the cloud. During the second day, several speakers show what they use Galaxy for and how they managed to implement their tools into Galaxy.

The last day was a very interactive day discussing the latest developments in Galaxy. Have a look at the wiki pages for copies of the presentations.

We would like to thank for the financial support we got from SystemsX.ch and for all the help we got from the Galaxy team, especially for sending Dannon over to Europe. It was great to have him, and the event profited a lot from him.

Running the event at two different places caused some logistical problems - some participants even learned about European geography. But the event was again a great success and we got a lot of great feedback. We are looking forward to the next Swiss German Galaxy Tour.

Björn and Hans-Rudolf

Posted to the Galaxy News on 2014-10-21

BioBlend v0.5.2 has been released. 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.)

This is mostly an incremental bug fix release with the following summary of changes:

  • BioBlend.objects: enable email & password authorization

  • Enable ToolShed tar ball uploads

  • BioBlend.objects: allow deletion of history and library datasets

  • BioBlend.objects: fixed library dataset downloads

  • Fixed the ToolShed tool installation method

  • Add 'deleted' attribute to DatasetContainer

  • Handle data_type changes in the Oct 2014 Galaxy release
  • Renamed get_current_history() to get_most_recently_used_history()
  • A number of documentation improvements and other small fixes

See the commit messages for more details.

Enjoy and please let us know what you think,

Enis & John & Simone Leo & Nicola Soranzo & The Galaxy Team

Posted to the Galaxy News on 2014-10-17

Galaxy Training Network

We are pleased to announce the Galaxy Training Network (GTN), a network of trainers who teach bioinformatics using Galaxy, or teach about Galaxy itself. The GTN aims to make it easy to find Galaxy trainers, and to share and discover the wealth of training resources available for Galaxy. This includes training materials, a trainer directory,best practices, and guidance on computing platforms for teaching with Galaxy. The Galaxy Training Network is accessible to the entire community.

If you teach with Galaxy, then please consider adding your organization, materials, and best practices. The Trainer Directory already includes 16 organizations and there may be one (or 6!) near you.


The Galaxy Training Network (GTN)

Posted to the Galaxy News on 2014-10-16

The French Working Group GALAXY-IFB (Institut Français de Bioinformatique) is organizing a second session around the Galaxy portal.

The event will be at Institut Curie in Paris over two days. This year, we want to involve two communities: biologists (also known as Galaxy 'users') and bioinformaticians (Galaxy 'developers').

The goal is to present user experience around the portal, from a single user to a wider community:

  • Dec 2 (13:30-17:30): Galaxy's user experiences, and discussion on how the platform is (or is not) useful for building analysis.
  • Dec 3 (09:00-17:00): Technology talks (new environment, Galaxy in production, ...)

You are strongly encouraged to submit an abstract before October 31 to <ifb DOT galaxy AT sb DASH roscoff DOT fr>. The abstract should be in English (although the event will be in French) and 10/20 lines long. Please put "[Galaxy Day]" in the subject line.

The French IFB Galaxy Working Group:

URGI, GenoToul, MIGALE, PFEM, SouthGreen, Institut Curie, ABiMS

URGI   GenoToul   MIGALE   PFEM   SouthGreen Institut Curie   ABiMS

Posted to the Galaxy News on 2014-10-15

Galaxy Updates

A lot is happening in in the Galaxy in October, and a lot of good stuff happened in September too. Take a look at the October 2014 Galaxy Newsletter for the complete story, but here are some highlights:

Happy October!

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2014-10-01

The Galaxy Project is preparing for our next grant cycle and we are seeking your feedback and comments on on all things Galaxy. We have created two questionnaires, each focused on how you interact with Galaxy:

  1. Galaxy User Questionnaire

  2. Galaxy Admin, Tool Developer, and Galaxy Developer Questionnaire

Please take a few minutes and fill out whichever surveys apply to you. The questionnaires are structured so you can skip topics that don't apply to you, and every question is optional.

And, to thank you for your time and effort, the Galaxy Project will increase your storage quota on usegalaxy.org by 50GB, a 20% increase.

Let your voice be heard!

The Galaxy Team

Posted to the Galaxy News on 2014-09-30

usegalaxy.org will be intermittently unavailable 2014/09/20

usegalaxy.org, the Galaxy Project's public Galaxy Server will be intermittently unavailable between 10am - 6pm EDT (UTC -0400) on Saturday, Sept 20th, 2014 due to scheduled network maintenance. Execution of new jobs will be paused to prevent failures.

This outage will only affect the Galaxy Project public servers. Public Galaxy servers run by other groups will be unaffected by this outage.

Posted to the Galaxy News on 2014-09-13

   These workshops have been cancelled.   

Galaxy Workshops at 2014 ASA, CSSA, and SSSA International Annual Meeting

This year Galaxy will have a presence (for the first time) at the ASA, CSSA, and SSSA International Annual Meeting, being held in Long Beach, California, from November 1-5. Three workshops are being offered:

Introduction to Bioinformatics Analysis with Galaxy
Saturday, Nov. 1, 2:00 pm–4:00 pm
This hands-on workshop will introduce the Galaxy platform and walk participants through a multi-step analysis exercise using example genomic data. We will also cover basic bioinformatics topics such as common file formats and visualization. Participants will leave this workshop knowing how to do basic bioinformatics analysis on public Galaxy servers, and how to use Galaxy to explore and learn many other types of bioinformatics analysis. This workshop complements the later SNP/Variant Analysis with Galaxy and the A Gentle Introduction to Cloud Computing: Setting up your own Galaxy Server workshops.
Price: $30 ($40 after Sept. 17)

SNP/Variant Analysis with Galaxy
Sunday, Nov. 2, 8:00 am–12:00 pm
This hands-on workshop will walk participants through a multi-step SNP and variant data analysis exercise using next generation sequencing (NGS) data generated from crops. The workshop will introduce NGS data formats and quality control and then walk through the analysis within the context of Galaxy, taking full advantage of Galaxy’s rich tool set and visualization capabilities. The workshop assumes no knowledge of command line interfaces or programming and will not use either. This workshop complements the earlier Introduction to Bioinformatics Analysis with Galaxy and subsequent A Gentle Introduction to Cloud Computing: Setting up your own Galaxy Server workshops. While attendance at the prior workshop would be helpful it is not required to attend this workshop. Galaxy is a web-based, open-source project funded by NIH. There are currently over 50 publicly accessible servers around the world and across the tree of life. Galaxy can also be installed locally, or on the cloud, and commercial support is offered by several vendors.
Price: $60 ($80 after Sept. 17)

A Gentle Introduction to Cloud Computing: Setting up your own Galaxy Server
Sunday, Nov. 2, 2:00 pm–5:00 pm
Cloud computing is an affordable way to support the widely variable and ad hoc nature of bioinformatics analysis that does not require setting up or maintaining local compute clusters.
This talk will briefly introduce basic cloud concepts and the Galaxy CloudMan package. We’ll then run a hands-on demonstration where each participant will set up a Galaxy server on Amazon Web Services (one of the several cloud infrastructure options) using CloudMan, add a dynamically scalable compute back-end cluster to perform analysis, customize the server by adding new tools, run a basic analysis using crop data that we load onto the server, and then shut the server down when we no longer need it. All steps will be done thorough a web browser, without ever using a command line interface.
This workshop complements the earlier Introduction to Bioinformatics Analysis with Galaxy and SNP/Variant Analysis with Galaxy workshops. Attendance at the prior workshops is not required to attend this workshop. In addition to being available on the cloud, Galaxy is open-source and can be installed locally. There are over 50 publicly accessible Galaxy servers and hundreds of private installations around the world.
Price: $35 ($45 after Sept. 17)

Early registration ends in two weeks, on September 17. After that workshop registration rates go up by as much as 30%. The meeting is being held in Long Beach, California, United States, from Nov 1-5.

Please let us know if you have any questions, and we hope to see you there.

Dave C

Posted to the Galaxy News on 2014-09-03, updated 2014-09-23

Galaxy IRC Channel

We would like to change the logging policy for the #galaxyproject IRC channel:

Currently, this channel is not logged anywhere. This change will only be made if the community agrees that a searchable online log would be an improvement. If you have thoughts or comments on this proposal, then please post them to this Biostar thread. In two weeks' time (around September 17, 2014), we'll summarize the discussion and publish a decision.

Proposal Details:

Starting sometime after community discussion ends (and assuming that discussion is favorable):

  1. At least two weeks before the change:
    1. Warnings will be added to the IRC channel information and on the wiki, that the log will be publicly archived as of the given start date.
    2. The policy change will be announced on Galaxy Biostar and the Galaxy-Dev and Galaxy-Announce mailing lists.

  2. On the launch date
    1. The IRC channel (and the wiki) will be updated to clearly state that the IRC channel is publicly logged.
    2. Announcements of the change will be posted to Biostar and the mailing lists.
    3. IRC postings from the announcement onward will start showing up in the public log.
    4. The IRC channel log will be included in the Galaxy search engines.

Why now?

The project's IRC channel came up at the GalaxyAdmins BoF meetup at GCC2014, where it was lauded as both a great resource, and cursed because it is not archived anywhere. An action item from that meetup is to propose this change.

The Galaxy Team

Posted to the Galaxy News on 2014-09-02

Galaxy Updates

Hello all,

A lot of cool stuff happened in the Galaxy in August, and even more cool stuff is coming: The September Galaxy Newsletter is out and here are some highlights:

And, as always, there are new papers, new jobs, and a double dose of new ToolShed contributions.

Happy September,

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2014-08-29

Dear UK Galaxy-devs,

We're delighted to announce the launch of the UK Galaxy Community.

Please visit the site and have a look around:

The aims of Galaxy-UK are:

  • To bring the Galaxy community in the United Kingdom closer together
  • Identify and address the needs of the community
  • Encourage interaction and collaboration.

Galaxy-UK is also an information hub for events such as:

We will be organising both online meetings and physical meetings, so keep an eye on the site for these events.

Best wishes,

The Galaxy-UK Team

Galaxy-UK Community is Live!

Posted to the Galaxy News on 2014-08-14


Complete News Brief


Security alert from July 31st, upgrade now
Citations: DOIs, BibTeX, and much much more
Docker: You voted, we've got it, with a little help from our friends (you!)
• Significant Workflow, API, Job, Tool Shed, and Dataset management updates
• Fixes, tunings, plus just a drop of → Gossip






$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable 


$ hg pull 
$ hg update latest_2014.08.11

Thanks for using Galaxy!

The Galaxy Team

Posted to the Galaxy News on 2014-08-11


We just released an update to Galaxy CloudMan. 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.

This is mostly an incremental bug fix release with the following summary of changes:

  • On AWS, updated galaxyFS snapshot (snap-e6e1c04a), which includes the June 2, 2014 Galaxy release with the July 30th security fix. All the tools installed via the Tool Shed have been updated and a number of new tools added, most notably: Tophat2, Bowtie2, FastQC, several FASTQ manipulation tools, several QC tools.
  • For AWS, added support for VPC
  • For OpenStack clouds, added the ability to automatically recover worker instances on cluster reboot

  • Added support for creating a file system based on a downloadable archive
  • Do not run Galaxy with multiple processes by default. This is because Tool Shed installs do not work properly in the multi-process mode. This feature can be enabled by setting user data option configure_multiple_galaxy_processes to True when launching an instance.

  • Set SGE slots in each queue to be equal to the number of cores on the instance
  • Set instance IP in the Galaxy's FTP data upload tool message
  • Added support for Nginx v1.4 and allow it (with the PAM module) to used as the authentication mechanism when accessing Galaxy Reports app
  • Fixed cluster deletion when performed via the API
  • No longer automatically start Hadoop and HTCondor services
  • On manually-invoked instance reboots, do not increment the instance reboot count that otherwise eventually leads to instance termination
  • Limit the size of the log message buffer used in the UI to 1000 lines. Long-running instances had issues with this log growing large and that led to poor UI performance. The complete log is still available from the Admin page (or the command line).
  • Automatically delete the bucket/container for Test type (i.e, 'SGE only') clusters on cluster termination

For complete details on implemented changes, please see the source code commits.

Enjoy and please let us know what you think,

Enis & Dannon & The Galaxy Team

Posted to the Galaxy News on 2014-08-08

Galaxy Updates

The August 2014 Galaxy Update Newsletter is out. Here's a preview of what's inside:

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2014-08-01

Galaxy Updates

GCC2014: June 30 - July 2

BOSC 2013 ISMB 2014

The July 2014 Galaxy Update Newsletter is out, and a few days early at that. Here's a preview of what's inside:

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2014-06-25

Dataset Collections Workflow Detail
example dataset collection workflow (credits)

News Brief Highlights:

  • Dataset Collections introduced
  • Changes to database build (dbkey) organization
  • Enhancements to Tool configuration and Workflow options
  • Trackster, User Interface, and Admin panel upgrades
  • Significant updates to Admin and Job functionality
  • Tool Shed repository and API additions
  • Data updates plus new Security features and Bug fixes






$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable 


$ hg pull 
$ hg update latest_2014.06.02

Thanks for using Galaxy!

The Galaxy Team

Posted to the Galaxy News on 2014-06-02

Galaxy Updates

GCC2014: June 30 - July 2
GCC2014 Hackathon

The June 2014 Galaxy Update Newsletter is out! There's a lot going on in the project and the community right now. The big news for the coming month is

There are also at least 14 other Galaxy related events in the next two months in Thailand, Canada, France, the United States, Italy, the Netherlands, Australia, and Brazil.

And, in the past month there were:

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2014-05-30

Two postdoc positions

Two postdoc positions are available in Oslo, Norway on the development of genome analysis methodology integrated with the Galaxy platform. The aim is to pioneer the development of sophisticated and streamlined software systems for broad use cases within integrative genomics, where the specification is deliberately somewhat broad in order to allow the visions of candidates to influence the exact direction.

The hired postdocs can exploit the Galaxy framework to ensure accessibility, interoperability and reproducibility for the systems they develop, and can further exploit the robust data management and statistical analysis functionality of the Genomic HyperBrowser framework (which is a separate, 90 000 line code base integrated with Galaxy). The positions are embedded within the HyperBrowser environment, which includes seven researchers and programmers working primarily on the development of genome analysis functionality, as well as around thirty more loosely coupled collaborators. For more on the HyperBrowser, check out an overview paper of previous developments, or try out our public server. 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.

Geir Kjetil Sandve

Posted to the Galaxy News on 2014-05-27

usegalaxy.org offline May 24 31, 2014

usegalaxy.org will be down 2014/05/31

Access to all TACC-based resources and services, including usegalaxy.org and the Galaxy Project Test Server, will be unavailable from 9 a.m. to 5 p.m., central US time, on Saturday, May 24 31, 2014. TACC staff will be performing an upgrade to the networking infrastructure. During this time, jobs will continue to run.

During this time you are encouraged to use any of the 60+ public Galaxy servers.

Posted to the Galaxy News on 2014-05-16, updated 2014-05-21

Galaxy Updates
Galaxy Biostar

GCC2014: June 30 - July 2

UK May 2014 Galaxy Tour   GCC2014 Hackathon

The May 2014 Galaxy Update Newsletter is out! There's a lot going on in the project and the community right now. The big news in the past month is the move from the Galaxy-User mailing list to Galaxy Biostar for user support. This has been running for a week now, and has been very well received.

The other big news is upcoming events. Early registration for GCC2013 closes May 23. Register now and save more than 70% on registration costs, and Training Day registration is an additional 55% off if you register for both at the same time. We are also pleased to announce this year's keynote speaker and the first ever GCC Hackathon.

There's also a Galaxy UK Tour which is visiting Norwich and Edinburgh in May, and there are at least 17 other Galaxy related events in the next 70 days in Norway, France, online, Croatia, Thailand, Canada, the US, the Netherlands, and Australia

As always, there are new papers (47 of them, including four we highlighted), new public Galaxy Servers (Globus Genomics Proteomics and SunLab Galaxy), new jobs (7 postings in 6 countries), new tools in the project ToolShed (um, lots), and a new public ToolShed (at the Dutch Techcentre for Life Sciences (DTL).

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2014-04-30

Galaxy Biostar

Galaxy has teamed up with Biostar to create a Galaxy User support forum at https://biostar.usegalaxy.org!

We want to create a space where researchers using Galaxy can come together and share both scientific advice and practical tool help. Whether on usegalaxy.org, a CloudMan instance, or any other Galaxy (public or local), if you have something to say about Using Galaxy, this is the place to do it!

Current integration with usegalaxy.org

  • We imported the whole history of the galaxy-user@bx.psu.edu mailing list into Galaxy Biostar. Your prior posts are automatically claimed when you login!

  • If you access Galaxy Biostar from http://usegalaxy.org (Menu: Help → Galaxy Biostar) you will be automatically logged in. A Galaxy Biostar account will be created for you if it did not previously exist. To obtain this account’s password please use the password reset feature of Galaxy Biostar.

  • When you have a question, search Galaxy Biostar directly from any Galaxy tool page.

Read more about how to get started on the Biostar wiki page.

Roll-out phase

What’s next

We hope you will like the change and look forward to any feedback you may have.

Thank you for using Galaxy!

Galaxy Team

Posted to the Galaxy News on 2014-04-23

GCC2014 Hackathon

Galaxy has a fantastic developer community, from the very active mailing lists and #galaxyproject IRC channel to individuals who have submitted literally hundreds of pull requests and patches. We are always looking for ways to interact with existing community members and get even more people involved. To that end, we’re thrilled to officially announce the very first Galaxy Project Hackathon. The hackathon will be a three day event taking place at Johns Hopkins immediately preceding GCC2014 from June 28th-30th.

Do you have a feature you've always wanted to implement? Just want to hack on Galaxy (or CloudMan!) with other folks? The Galaxy Hackathon will be a great opportunity to meet and work closely with other community and Galaxy Team members over the course of three days, culminating in some really great improvements and new features to show off at the Galaxy Community Conference afterward.

Participation in the hackathon itself is completely free, but there's limited space so if you're interested and would like to participate please go ahead and book both your lodging and hackathon seat at EventBrite.

To help organize ideas and people into more concrete projects, we've also set up a hackathon-specific Trello board that we'd love for everyone to go ahead and start using it. The board is public and open to commentary and voting, but to create new cards you’ll need to be added as a member so please note the instructions on the board for that.

Finally, we are very happy to have Curoverse on board as the exclusive Peta level sponsor of the hackathon. If you know of any other group that might be interested in sponsoring at the Giga level please let us know.

We hope to see you in June, and can't wait to see what we can accomplish!

-Dannon Baker on behalf of the GCC2014 Hackathon Organizing Committee

Posted to the Galaxy News on 2014-04-18

Trackster Vis

  • Trackster deep coverage view

News Brief Highlights:

  • Visualization framework and Trackster display enhancements
  • Tool Shed upgrades for repos, installs, tests, and docs
  • Over 100 genomes with new content on our rsync server
  • UI unification of design plus expanded dataset action access
  • API functionality additions including new job control/admin abilities
  • More features for admin functions, config options, and job controls
  • 18 new community contributions incorporated (big thanks!)






$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable 


$ hg pull 
$ hg update release_2014.04.14 

Thanks for using Galaxy!

The Galaxy Team

Posted to the Galaxy News on 2014-04-14

Galaxy Australasia Workshop 2014 CSIRO

A Conference Report for the first Galaxy Australasia Workshop is now available. Most of the slides and posters are also available.

The first Galaxy Australasia Workshop (GAW 2014) was held on Monday 24th and Tuesday 25th March. Conference venues and catering were provided by CSIRO (Australia's national science agency) so attendance was free.

The event featured more that twenty keynotes, accepted presentations, posters, tutorials, and panel discussions. The event was attended by over forty people from over twenty organizations and at least three continents. See the Conference Report for full details.


Ron Horst

Posted to the Galaxy News on 2014-04-09

April 2014 Galaxy Update

GCC2014 early registration and abstract submission are now open

Happy April everyone!

It's a busy time in the Galaxy and that is reflected in the April 2014 Galaxy Update. First, there were a record 63 new papers in the past month, six of which we have highlighted (also a record). Three new public Galaxy servers, and one Galaxy Community Log Board entry were also added in March.

However, the big news this month is Upcoming Events:

And as always, there are new ToolShed contributions and other news as well.

If you have anything you would like to see in the next Galaxy Update, please let us know.

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2014-03-31

Globus World 2014

GlobusWorld is this year’s biggest gathering of all things Globus. GlobusWorld 2014 features a features a Using Globus Genomics to Accelerate Analysis Tutorial, and a full half day on Globus Genomics in the main meeting, including a keynote by Nancy Cox and these accepted talks:

  • Globus Genomics: Enabling high-throughput cloud-based analysis and management of NGS data for Translational Genomics research at Georgetown, by Yuriy Gusev,

  • Improving next-generation sequencing variants identification in cancer genes using Globus Genomics, by Toshio Yoshimatsu

  • Globus Genomics: A Medical Center's Bioinformatics Core Perspective, by Anoop Mayampurath

  • Building a Low-budget Public Resource for Large-scale Proteomic Analyses, by Rama Raghavan

Globus Genomics is a Globus and Galaxy based platform for genomic analysis. GlobusWorld is being held April 15-17, in Chicago. And, GCC2014 is a Silver Sponsor of GlobusWorld.

Ravi Madduri

Posted to the Galaxy News on 2014-03-28

50+ Public Galaxy Servers that will not be affected by this outage

Access to all TACC resources and services, including UseGalaxy.org, will be unavailable between 9 a.m. - 5 p.m. (US Central Time) on Saturday, March 22. TACC staff will be performing an upgrade to the networking infrastructure.

During this outage, users are encouraged to use the 50+ other public Galaxy servers that won't be affected by this upgrade.

Posted to the Galaxy News on 2014-03-17

GCC2014 Training Day

We are pleased to announce that Early Registration and Talk and Poster Abstract Submission are now open for the 2014 Galaxy Community Conference (GCC2014).

GCC2014 will be held at the Homewood Campus of Johns Hopkins University, in Baltimore, Maryland, United States, from June 30 through July 2, 2014. GCC2014 starts with a Training Day featuring four five parallel tracks, each with three, two and half hour long workshops. There are 13 different topics spanning the full Galactic spectrum of topics. Take a look!

Early registration is now open. Register early and avoid paying 70% more for regular registration costs.  Early registration is very affordable, with combined registration (Training Day + main meeting) starting at $140 for post-docs and students. Registration is capped this year at 250 participants, and we expect to hit that limit. Registering early assures you a place at the conference and also a spot in the Training Day workshops you want to attend.

You can also book affordable conference housing at the same time you register. See the conference Logistics page for details on this and other housing options.

Abstract submission for both oral presentations and posters is also open.  Abstract submission for oral presentations closes April 4, while poster submission closes April 25. Poster authors will be notified of acceptance status within two weeks of submission, while presentation authors will be notified no later than May2.  Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.

GigaScience Journal

The GigaScience "Galaxy: Data Intensive and Reproducible Research" series announced for the last conference has published its first papers, and is continuing to take submissions for this year's meeting and beyond. BGI is also continuing to cover the article processing charges until the end of the year, and for more information see their latest update.

Thanks, and hope to see you in Baltimore!

The GCC2014 Organizing Committee

Posted to the Galaxy News on 2014-02-14

Complete News Brief

  • Visualization upgrades, including Trackster CSS styling
  • Multiple Tools migrated to the Tool Shed for a leaner distribution
  • Redesign of UI rendering: new icons, new font, history pane updates
  • API functionality upgrades featuring a new master admin API key
  • Tool Shed updates a focus on repository metadata, displays, installs, and tests
  • Over 35 new community contributions added




new:       $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable

upgrade:   $ hg pull 
           $ hg update release_2014.02.10

Thanks for using Galaxy!

The Galaxy Team

Posted to the Galaxy News on 2014-02-10

Google Summer of Code 2014

The Galaxy Project will be applying for Google Summer of Code 2014 as part of the Genome Informatics Group. We are looking for project proposals to include in the group's submission to Google. Please submit your proposals by January 31.

If you are interested in submitting an idea, or being a mentor then please email Robin Haw <robin DOT haw AT oicr DOT on DOT ca> and <outreach AT galaxyproject DOT org>. There is also a mailing list and an IRC channel: #genomeinformatics on Freenode.

The Genome Informatics Group is organizing the joint efforts of Galaxy, GMOD, Reactome, SeqWare, and Wormbase. This is a great opportunity for students to contribute to the work of any of these established bioinformatics projects.

If your interests lean more towards toolkits, I would like to point out that the Open Bioinformatics Foundation (OBF), the group behind the Bio* toolkits (including BioPython) and the BOSC conferences, is also looking for people to coordinate their proposal.

Dave Clements

Posted to the Galaxy News on 2014-01-18

The 1st Galaxy Australasia Workshop 2014 (GAW 2014) will be held in Melbourne, Australia on 24 and 25th March 2014.

Galaxy Australasia Workshop 2014

The Galaxy Australasia Workshop is a great opportunity for you to participate in two full days of presentations, discussions, poster sessions, keynotes and lightning talks, all about ways of using Galaxy for high-throughput biology, imaging and other scientific applications. The workshop will also include Training Sessions taught by Galaxy developers and master users. GAW 2014 will run 24 and 25th March, immediately preceding Computational and Simulation Sciences and eResearch in Melbourne.

GAW 2014 will also include poster session, keynote speakers.

You should attend to:

  • Present your work!
  • Learn best practices for deploying Galaxy, defining and installing resources, and managing and moving large datasets.
  • Network with others in the Galaxy community who are facing similar challenges and using Galaxy and other tools to address them.
  • Learn what the Galaxy Project's plans are, and contribute to Galaxy's future direction.
  • Learn
    • how to visualize your data in Galaxy and use visualization to guide your analysis (visual analytics)
    • how to share, publish, and reuse your analyses with Galaxy
    • how to perform and enable your users to perform common, yet complex, analyses using Galaxy
    • when and how to use Galaxy on the Cloud

Topics will potentially include:

  • Image analysis and processing using Galaxy.
  • RNAseq/ChIPseq/Variant Calling/RNA Quality Control.
  • Galaxy on the Research Cloud.
  • CSIRO galaxy service - partnership between science and IT.
  • Identifying proteins from mass spec data with Galaxy.

Call For Abstracts

Participants who wish to give presentations or present posters (potentially with technical demonstrations) that showcase use of Galaxy should submit a brief one-page abstract and brief one-paragraph bio to the GAW2014 Organisers <gaw2014 DASH org AT groups DOT galaxyproject DOT org> by February 15th, 2014. Submitters will be notified by February 28th. Speakers, panelists, and poster presenters will be selected by the program committee based on relevance to symposium objectives and workshop balance.

Submissions should clearly state whether they are for: poster or oral presentation.

Looking forward to seeing you all in Melbourne!

GAW 2014 Organising Committee

Posted to the Galaxy News on 2014-01-17


We just released an update to Galaxy CloudMan. 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.

This update brings a large number of updates and new features, the most prominent ones being:

  • On AWS, updated galaxy (snap-69893175) and galaxyIndices (snap-4b20f451) file system snapshots, which include the Nov 4, 2013 Galaxy release as well as a significant number of Galaxy tools updates and additions. Tool installations from the Tool Shed work as expected.

  • Updated the AWS AMI: Galaxy CloudMan 2.3 (ami-a7dbf6ce)

  • Made multi-process Galaxy the default option for running Galaxy with CloudMan.

  • Automatically toggle master as job execution host or not when workers are present.
  • Added support for attaching external Gluster based filesystems + the ability to init clusters off gluster/nfs volumes when so configured in snaps.yaml.

  • Added support for creating a volume based on an archive_url allowing a file system to be downloaded at cluster launch; also made it possible to use transient disk for this.

  • Added tagging support for OpenStack instances (requires OpenStack Havana release).

  • Galaxy Reports app now starts by default on Galaxy type clusters; it is accessible on <instance IP>/reports/ URL.

Minor updates

  • Added AWS new High I/O instance types.
  • Created proFTPd service for managing the application; fixes occasional issues with FTP connectivity

  • Updated admin_users (in Admin) form data-prefill and explanatory text to indicate correctly that this form now sets all admin users, instead of appending to the existing list.

  • Included cluster name into the page title.
  • Explicitly indicate that upon cluster deletion shared clusters get removed too.
  • Added TMPDIR env var to point to a dir on (Galaxy's) data file system.

  • Generalize support for finding libc on newer Ubuntu platforms. Allows CloudMan to run on Ubuntu 13.04 and tries to be future compatible with new minor releases of libc (thanks Brad Chapman).

  • Numerous fixes, see commit log for details.

For more details on the new features, see the the CHANGELOG and for even more details see, all 103 commit messages from 4 contributors.

Enjoy and please let us know what you think,

Enis Afgan and Dannon Baker

Posted to the Galaxy News on 2014-01-07

GCC2014 Training Day

What topics should be offered at the GCC2014 Training Day?

Topics for the GCC2014 Training Day are selected by you, the Galaxy Community. For GCC2014 there are 19 nominated topics to pick from. Your votes will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters.

Topic voting closes January 17. The Training Day schedule, including instructors, will be published before early registration opens on February 10.

   Vote now!   

About the GCC2014 Training Day:

The 2014 Galaxy Community Conference (GCC2014) will start on June 30 with a Training Day featuring 4 parallel tracks, each with three workshops, each of which are two and a half hours long, for a total of twelve sessions. There will be at least one complete track (3 consecutive workshops) about using Galaxy for biological research, and at least one full track on deploying and managing Galaxy instances.

As always, please let us know if you have any questions.


The GCC2014 Organizing Committee

Posted to the Galaxy News on 2014-01-07

January 2014 Galaxy Update

Galaxy Community Log Board

Galaxy Deployment Catalog

The January 2014 Galaxy Update is out!

If you have anything you would like to see in the next Galaxy Update, please let us know.

Best wishes to you and yours for a happy and spectacular 2014,

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2013-12-31