November 2017 Galaxy News

Galaxy News

Welcome to the November 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.


The Galactic Blog

The Galactic Blog is born

The new Galactic Blog was launched in October. The Galactic Blog is a place for longer-form posts that are relevant to Galaxy. (See Galaxy News for shorter-form items.) The Galactic Blog replaces the former Community Log and includes all content from it, which is why, even though the blog is new, it includes entries back to 2013.

The blog is off to a running start with these posts in October:

The Galactic Blog needs you!

The Galaxy community needs to know what you are doing. If you have done something that others would benefit from knowing then please create a Galactic Blog post describing your experiences.

Blog posts can either be directly created on the Hub, or can be posted on your favorite blogging platform and linked to from the Blog home page. See the CONTRIBUTING page for how.

Questions? Ask us.

Publications

The Galaxy Publication Library surpassed 5,000 publications, in October. It was a good month for publications in other ways too:

Highlighted Publications

The Galactic and Stellar publications added in October were:

Publication Topics

110 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library in October.

# Tag # Tag # Tag # Tag
56 +Methods 17 +RefPublic 16 +Workbench 16 +UsePublic
15 +UseMain 10 +UseLocal 9 +Reproducibility 9 +Tools
5 +IsGalaxy 4 +HowTo 4 +Shared 3 +Cloud
3 +Unknown 1 +Project

We also added tags to papers that reference, use, or implement a Galaxy Public Server. See below for this list.


Events

Galaxy (and GMOD) at Plant and Animal Genome XXVI

Galaxy at PAG XXVI

The 26th Plant and Animal Genome Conference will be held January 13-17, in San Diego, California. PAG is the largest ag-genomics meeting in the world and Galaxy will be there to help researchers get the most from their data. There will be a Galaxy Workshop with 4 talks, and a Galaxy Community Update talk during the GMOD session. See the Galaxy @ PAG page for details. (We'll also list Galaxy related posters and Digital Tools and Resources talks once they are scheduled.)

GMOD @ PAG

GMOD at PAG XXVI

GMOD (of which Galaxy is a part) has a bunch of things going on at PAG that are of interest to the Galaxy Community:

If you are interested in supporting better integration of Galaxy with other GMOD components then please give the two hackathons a look.

Deadlines
Oct 31 PAG Early registration ends
Nov 10 Digital Tools and Resources and Poster track abstract submission ends

Upcoming events

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


Date Topic/Event Venue/Location Contact
November 1st 2017 Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter Genome Informatics, CSHL, New York, United States Anton Nekrutenko
November 1st 2017 Hybrid assembly of small genomes in Galaxy Genome Informatics, CSHL, New York, United States Delphine Lariviere
November 3rd 2017 Adapting Galaxy for language processing Monthly Tech Talk: Scientific Workflow Systems, Online (Australia) Steve Cassidy
November 4th 2017 Introduction to Galaxy: A Bioinformatics Platform for Research and Classroom Use, a K-INBRE Bioinformatics Workshop Kansas State University, Manhattan, Kansas, United States Sherry Miller
November 6th 2017 RNA-seq data analysis (7th edition) Leiden University Medical Center, Leiden, The Netherlands Training offered by GTN MemberPeter-Bram 't Hoen, Leon Mei, Jan Oosting, Szymon Kielbasa
November 15th 2017 RNA-Seq analysis using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
November 15th 2017 Analyse de données RNA-seq sous l’environnement Galaxy Lyon, France Training offered by GTN MemberC. Oger, P. Veber, Dr. V. Lacroix
November 17th 2017 Turning Bioconductor workflows into Galaxy tools Adelaide, Australia Maria Doyle
November 20th 2017 Quality Control of Next Generation Sequencing Reads University of Aberdeen, Scotland, United Kingdom Training offered by GTN MemberSophie Shaw
November 29th 2017 Foundations of Computational Genomics Course CSHL, Cold Spring Harbor, New York, United States Training offered by GTN MemberJames Taylor
November 30th 2017 Genome Assembly and Annotation University of Aberdeen, Scotland, United Kingdom Training offered by GTN MemberSophie Shaw
January 8th 2018 European Galaxy Administrator Workshop Oslo, Norway Training offered by GTN Member
January 13th 2018 Plant & Animal Genome XXVI (PAG 2018) San Diego, California Training offered by GTN MemberSee web page
April 22nd 2018 The Galaxy Platform as an Accessible, Core Laboratory Solution for Proteogenomic Analysis and Informatics ABRF 2018, Myrtle Beach, South Carolina, United States Training offered by GTN MemberPratik Jagtap
June 25th 2018 GCC2018 & BOSC 2018 Reed College, Portland, Oregon, United States Training offered by GTN MemberOrganizers

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


Who's Hiring

Please Help! Yes you!

The Galaxy is expanding! Please help it grow.

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.


Public Galaxy Server News

There are over 90 publicly accessible Galaxy servers and six semi-public Galaxy services. Here's what happened with them in October.

Public Servers in October's Publications

As part of the move to Zotero, we have started tagging papers that use, mention, implement or extend public Galaxy Servers with the server name. Here are the counts for October's papers.

# Server # Server # Server # Server
10 >Huttenhower 3 >Workflow4Metabolomics 2 >VirAmp 2 >GVL-Unspecified
2 >WUR 2 >GVL-QLD 1 >Whale Shark 1 >Jetstream
1 >RiboGalaxy 1 >BF2I-MAP 1 >APOSTL 1 >GIO
1 >BioCiphers 1 >DeepTools 1 >ARGalaxy 1 >RepeatExplorer
1 >Oqtans 1 >BioMaS 1 >ABiMS

Citation sections added to Public servers directory

The public Galaxy server directory was updated in October to include a Citation(s) section for each server. If you use a server in your research, then please cite it.

BF2I-MAP

BF2I-MAP

The BF2I-MAP server features locally developed (as well as standard tools) including ThreaDNA, which "allows generalising the approach to a large class of DNA-binding proteins." (Cevost et al.). BF2I-MAP is supported by the Laboratoire de Microbiologie, Adaptation et Pathogénie, Biologie Fonctionnelle Insectes et Interactions, L'Université Claude Bernard Lyon 1, and INSA de Lyon

Citations

Almost a public server: Language Analysis Portal

UiO Language Analysis Portal

One of this month's highlighted papers (Kouylekov et al) describes the Language Analysis Portal, which is built on Galaxy and is described as:

The UiO Language Analysis Portal (LAP) enables non-technical end users to employ state-of-the-art tools for natural language processing processing (NLP) at the click of a few buttons; a typical scenario is for a user to upload some ‘raw’ textual data, invoke LAP linguistic analysis tools to create annotations of the text, export processing results into a format suitable for analysis by the user, and download the resulting file(s) back onto their own computer.

LAP is part of the national implementation in Norway of the European Common Language and Technology Infrastructure (CLARIN).

It's always great to see Galaxy applied in non-genomic domains, and LAP is a great example of how this can be done. Unfortunately, it falls just short of the definition of a public Galaxy server. Alas, it is accessible to many, but not all academic users. So we recommend taking a look at it, but we can't list it in the directory.


Tools

ToolShed Contributions

Galaxy ToolShed

Tool Shed contributions in October.

Releases

StarForge 0.3.1-5

StarForge help build Galaxy things in virtualization:

  • Build Galaxy Tool Shed dependencies
  • Build Python Wheels (e.g. for the Galaxy Wheels Server)
  • Rebuild Debian or Ubuntu source packages (for modifications)

These things will be built in Docker. Additionally, wheels can be built in QEMU/KVM virtualized systems. StarForge has had several updates this fall. Fixes and new features include:

  • Support xz/lzma tarballs for wheel builds Pull Request 166
  • Native support for auditwheel and delocate. (#160)
  • Do not build sdists with the wheel subcommand by default. (#155)
  • Fix a bug where the wrong working directory was set when building wheels with multiple sources. (#154)
  • Fix a bug with sudo and brew install on macOS. (#151).
  • Short circuit platform caching on OS X (#150).

sequence_utils 1.1.2

Galaxy's sequence utilities are a set of Python modules for reading, analyzing, and converting sequence formats. See the release notes for what's new this month.

Earlier Releases

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

Planemo 0.45 - 0.46.1

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.

BioBlend 0.10.0

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 0.10.0.

galaxy-lib 17.9.4-9

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:

  • Latest updates from the upcoming 17.09 release - including updating the default target Conda version and fixes for module resolution.
  • Updated CWL utilities.
  • Remove command lint check that is no longer valid.
  • Bring in various Galaxy updates including numerous Conda fixes and changes (thanks to @nsoranzo.
  • Improved error handling when parsing tool reStructuredText (thanks to @erasche).

Pulsar 0.8.0

Pulsar

A Pulsar update was released in September. Pulsar is a Python server application that allows a Galaxy server to run jobs on remote systems (including Windows) without requiring a shared mounted file systems. Unlike traditional Galaxy job runners - input files, scripts, and config files may be transferred to the remote system, the job is executed, and the results are transferred back to the Galaxy server - eliminating the need for a shared file system.

This release adds several features and 4 bug fixes.

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.

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.

May 2017 Galaxy Release (v 17.05)

GalaxyProject

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

And the rest ...

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


Other News