[](/galaxy-updates/)

Welcome to the September 2017 Galactic News, a summary of what is going on in the Galaxy community. If you have anything to add to next month's newsletter, then please send it to outreach@galaxyproject.org.

New Publications

122 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy CiteULike Group in August.

Some highlights from the recently added pubs:

• 2017 Galaxy community update Dan Blankenberg, Jeremy Goecks. F1000Research In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114388.1
• Approaches for small RNA-seq in Galaxy Mallory Freeberg, James Taylor. F1000Research In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114423.1
• Bio-Docklets: virtualization containers for single-step execution of NGS pipelines Baekdoo Kim, Thahmina Ali, Carlos Lijeron, Enis Afgan, Konstantinos Krampis. GigaScience, Vol. 6, No. 8. (August 2017), pp. 1-7, doi:10.1093/gigascience/gix048
• Building an open, collaborative, online infrastructure for bioinformatics training Bérénice Batut, Galaxy Training Network, Dave Clements, Björn Grüning. F1000Research In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114447.1
• Galaxy-compatible Tool for Rapid Aptamer Clustering and HT-SELEX Data Analysis Nikita A. Skrylnik, Asian Journal of Pharmaceutics (AJP), Vol. 11, No. 02. (2017), doi:10.22377/ajp.v11i02.1265
• Hack the Galaxy report Anthony Bretaudeau, Frederik Coppens, Hack the Galaxy Participants. F1000Research In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114391.1
• Integrative analysis of hundreds of datasets in Galaxy Geir K. Sandve, Boris Simovski, Sveinung Gundersen, Diana Domanska, Christin Lund-Andersen. F1000Research In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114523.1
• Making Galaxy user Interface Pluggable with Webhooks Evgeny Anatskiy, Anup Kumar, Helena Rasche, et al. F1000Research In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114475.1
• mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data Martin Larralde, Thomas N. Lawson, Ralf J. M. Weber, et al. Bioinformatics (07 April 2017), doi:10.1093/bioinformatics/btx169
• PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data Julian R. Garneau, Florence Depardieu, Louis-Charles C. Fortier, David Bikard, Marc Monot. Scientific reports, Vol. 7, No. 1. (15 August 2017), doi:10.1038/s41598-017-07910-5
• Pulling the Galaxy's strings Jeffrey Miller, Brenna Miller. F1000Research In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114436.1
• Recent object formation in the core of Galaxy Martin Čech, et. al. F1000Research In Bioinformatics Open Source Conference 2017, Vol. 6 (2017), doi:10.7490/f1000research.1114483.1
• Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data Chao Zhang, Jochem Bijlard, Christine Staiger, et al. F1000Research, Vol. 6 (16 August 2017), 1488, doi:10.12688/f1000research.12168.1
• The backbone of research reproducibility-sustainable and flexible tool deployment Björn Grüning, John Chilton, Johannes Köster, Dale Ryan, Yasset Perez-Riverol. F1000Research In Bioinformatics Open Source Conference 2017, Vol. 6 (2017), doi:10.7490/f1000research.1114482.1
• ToolDog-generating tool descriptors from the ELIXIR tool registry Kenzo-Hugo Hillion, Ivan Kuzmin, Hedi Peterson, Jon Ison, Hervé Ménager. F1000Research In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114473.1
• wft4galaxy: a workflow testing tool for galaxy Marco E. Piras, Luca Pireddu, Gianluigi Zanetti. Bioinformatics (24 July 2017), doi:10.1093/bioinformatics/btx461

Publication Topics

Upcoming events

There are a plenitude of Galaxy related events coming up in the next few months:

Date	Topic/Event	Venue/Location	Contact
September 7th 2017	Galaxy – a tool for analyzing NGS data: introduction	Ben Gurion University of the Negev, Beer-Sheva, Israel	Anton Nekrutenko
September 13th 2017	RNA-Seq analysis using Galaxy	QFAB, St Lucia, Queensland, Australia	training@qfab.org
September 25th 2017	Computational Genomics and RNA Biology	Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany	compgen@mdc-berlin.de
October 3rd 2017	Introduction to Galaxy & the Genomics Virtual Laboratory	Melbourne Bioinformatics, Carlton, Victoria, Australia
October 4th 2017	A primer for RNA-Seq processing, interpreting and visualization	University of Freiburg, Freiburg Germany	Steve Hoffmann, Olaf Wolkenhauer, Wolfgang Hess
October 4th 2017	RNA-Seq Differential Gene Expression Analysis using Galaxy & the GVL	Melbourne Bioinformatics, Carlton, Victoria, Australia
October 5th 2017	Variant Calling with Galaxy & the GVL for beginners	Melbourne Bioinformatics, Carlton, Victoria, Australia
October 18th 2017	SACNAS 2017 Pre-Conference Workshops	2017 SACNAS, Salt Lake City, Utah, United States	Camille Avestruz, Tracy Teal, Joslynn Lee, Dave Clements
October 20th 2017	Resources and Techniques for Training Students in Computational Skills	2017 SACNAS, Salt Lake City, Utah, United States	Camille Avestruz, Tracy Teal, Joslynn Lee, Dave Clements
October 23rd 2017	Demo: CloudLaunch as a Gateway for Discovering and Launching Cloud Applications	Gateways 2017, University of Michigan, Ann Arbor, Michigan, United States	Enis Afgan, Marcus Christie, Nuwan Goonasekera
October 23rd 2017	Analyse avancée de séquences	Carreire de l'Université Bordeaux Segalen, Bordeaux, France	Aurélien Barré, Raluca Uricaru, Benjamin Dartigues
October 23rd 2017	The Future Development of Bioinformatics in Germany and Europe	ZiF, Bielefeld University, Bielefeld, Germany	Rolf Backofen, Björn Grüning
November 29th 2017	Foundations of Computational Genomics Course	CSHL, Cold Spring Harbor, New York, United States	James Taylor
January 8th 2018	European Galaxy Administrator Workshop	Oslo, Norway
June 25th 2018	GCC2018 & BOSC 2018	Reed College, Portland, Oregon, United States	Organizers

See the Galaxy Events Google Calendar for details on other events of interest to the community.

Who's Hiring

The Galaxy is expanding! Please help it grow.

• Ingénieur en développement de composants Galaxy pour l’Ecologie, Station de Biologie marine, Concarneau, France
• Galaxy Project is hiring software engineers and postdocs at Johns Hopkins, Baltimore, Maryland, United States
• Ingénieur spécialisé en NGS, BIOGECO, Bordeaux, France
• Bioinformatics Research Associate, Huttenhower Lab, Harvard School of Public Health, Boston, Massachusetts, United States

Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the Galaxy News feed and include it in next month's update.

Takeru Galaxy

[](http://www.nabe-intl.co.jp/seq/takerugalaxy.html)

The Takeru Galaxy server is offered by NABE³ International, a manufacturer specializing in Linux-based clusters based in Tsukuba, Japan. Takeru Galaxy servers come as a fully configured (hardware and software) system featuring numerous standard biomedical analysis tools and reference genomes, all available in a Galaxy server. Customization and multiple support options are available.

Takeru Galaxy is the newest of many commercial support options for Galaxy.

Tools

ToolShed Contributions

[](http://toolshed.g2.bx.psu.edu/)

Tool Shed contributions in August.

Releases

nebulizer 0.4.2

Command-line utilities to help with managing users, data libraries and tools in a Galaxy instance, using the Galaxy API via the Bioblend library.

• Documentation
• Code

CAVEAT nebulizer is still a work in progress; please exercise caution when attempting irreversible operations especially against production Galaxy instances (for example when creating users or data libraries).

CloudBridge 0.3.3

CloudBridge aims to provide a simple layer of abstraction over different cloud providers, reducing or eliminating the need to write conditional code for each cloud. It is currently under development and is in an Alpha state.

Earlier Releases

Planemo 0.41.0 - 0.44.0

[](https://pypi.python.org/pypi/planemo/)

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. These releases included numerous fixes and enhancements.

See GitHub for details.

galaxy-lib 17.9.0-3

galaxy-lib is a subset of the Galaxy core code base designed to be used as a library. This subset has minimal dependencies and should be Python 3 compatible. It's available from GitHub and PyPi.

This set of revisions includes:

• Bring in latest Galaxy dev changes.
• Implement support for building Singularity mulled containers.
• Implement mulled version 2 package hashing.
• Fix default namespace for mulled operations from mulled to biocontainers.

gops 1.1.0

The Galaxy Operations Python Package now provides utilities for working with GFF files thanks to @bgruening and @nsoranzo.

Other packages that have been released in the prior 4 months.

May 2017 Galaxy Release (v 17.05)

The Galaxy Committers published the 17.05 release of Galaxy in May.

Galaxy Docker Image 17.05

The Galaxy Docker project has seen a new release, following Galaxy 17.05. Major features are an additional Docker compose setup with SLURM and HT-Condor deployments, BioContainers integration and much more automatic testing.

And

• The Galaxy Docker Project has reached more than 23k downloads on Dockerhub - not counting quay.io and all flavors

• From John Chilton:

  • Awesome new mode for docker-galaxy-stable by Björn Grüning: container scheduling with Condor

Parsec 1.0.0

Parsec is a newly released set of command-line utilities to assist in working with Galaxy servers. It uses automatically generated wrappers for BioBlend functions. Manage histories, launch workflows, and more, all from the command line. The README includes several examples.

BioBlend 0.9.0

BioBlend is a Python library for interacting with CloudMan and Galaxy‘s API. BioBlend makes it possible to script and automate the process of cloud infrastructure provisioning and scaling via CloudMan, and running of analyses via Galaxy.

See the release notes for what's new in release 0.9.0.

Galaxy CloudMan 17.05 on AWS

A new release of Galaxy CloudMan is available on the Amazon Web Services cloud infrastructure. This release includes Galaxy 17.05, an updated tool list, and Slurm configuration changes to improve job performance. To get started, vist https://beta.launch.usegalaxy.org/ or take a look at the Getting Started guide.

CloudLaunch

Technically, the all-new Galaxy CloudLaunch service has been in public beta since February but keep in mind that it will replace the current CloudLaunch service eventually so give it a try and let us know how it performs for you.

And the rest ...

Other Galaxy packages that haven't had a release in the past four months can be found on GitHub.

Other News

[](http://galaksio.readthedocs.io/en/latest/)

• Galaksio, an easy to use GUI for running Galaxy workflows. (And there is a video too.)