February 2018 Galaxy News

Galaxy News

Welcome to the February 2018 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.


Events

There are a plenitude of Galaxy related events coming up in the next few months, including large regional meetings in Europe and Africa.

GCCBOSC 2018 Training Topic Voting Closes Jan 31

GCCBOSC 2018: Vote for the Training Topics you want

Which is tomorrow. Vote now

Your vote 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.

GCCBOSC2018 will be held 25-30 June in Portland, Oregon, United States. It will feature two days of training: the second of which is multi-track and will feature content for both the BOSC and Galaxy communities. Workshops will be hands-on and participants will be strongly encouraged to bring a laptop and follow along. If you work in data-intensive biomedical research, there is no better place than GCCBOSC 2018 to present your work and to learn from others.

Thanks to everyone who nominated topics and helped write topic descriptions!

GCCBOSC2018 registration will open in February. Watch this space.

GCCBOSC 2018 Sponsors

We are happy to have announced several GCCBOSC 2018 sponsors in January. This month we are highlighting PeerJ:

PeerJ

PeerJ is proud to sponsor GCCBOSC 2018 and support the unified event for bioinformatics developers and practitioners. PeerJ's mission is to make Open Access affordable, fast, and easier for researchers and institutions, and central to this mission is our open source ethos. We publish two peer-reviewed journals, PeerJ and PeerJ Computer Science and we also host a free PeerJ Preprints server. PeerJ requires code to be open and accessible, hence readers can be assured that they can access the tools appropriately. We also provide open source tools helpful to both academics and general software development professionals.

GCCBOSC attendees may be interested to hear that, in addition to research articles, PeerJ welcomes articles describing bioinformatics software tools. These articles provide descriptions of new software tools (or significant new functionality in existing software) of interest to the bioinformatics and/or computational biology communities. You can browse the PeerJ Bioinformatics Software Tools Collection. Submit your bioinformatics manuscript here.

PeerJ is also excited to offer APC discounts to all GCCBOSC attendees - we'll be in touch with more details soon!


Download the one page summary. Download the full prospectus.

Call for sponsors!

Sponsors are a key part of GCCBOSC 2018. Is your organization interested in playing a prominent role in the first joint gathering of the Galaxy and BOSC communities? Then become a GCCBOSC 2018 sponsor and raise your organization's visibility in these active and engaged communities.

ELIXIR Galaxy Community Kickoff and Meeting, March, Freiburg

ELIXIR Galaxy Community Kickoff and Meeting
EMBL-Australia

The ELIXIR Galaxy community will have a kickoff meeting 14-16th March 2018, in Freiburg/Germany. We will combine this with a Galaxy User Conference and the official launch of the usegalaxy.eu server.

This event will also be coordinated with the EMBL Australia to also launch usegalaxy.org.au at the same time.

Wednesday (the 14th) will be dedicated to the ELIXIR Galaxy communtiy, to discuss and plan our roadmap in 2018 and 2019. Thursday and Friday (15th, 16th) will be a conference where Galaxy users talk about their research and use-cases. However, a few spots we will reserved for official talks from ELIXIR.

Register now as space is limited.

Galaxy Africa, April, Cape Town

Galaxy Africa

Galaxy Africa will be held 3-5 April in Cape Town, South Africa at SANBI on the Universtiy of the Western Cape campus.

This is an opportunity to learn from leading bioinformaticists, systems administrators and engineers about Galaxy and accessible, reproducible analysis of biological data.

  • Analyse: Learn about using Galaxy to analyse your genomic and RNA data.
  • Manage: Meet fellow admins of research computing infrastructure and hear about local and cloud hosting of Galaxy servers.
  • Extend: Hear how bioinformaticts are extending Galaxy through custom tools and workflows.

Our programme will start with keynote speakers introducing biology, data science and Galaxy. In the afternoon there will be tutorials on biological data analysis using Galaxy. The Wednesday morning session will include presentations on genomic and metagenomic data analysis workflows and uses of Galaxy. In the afternoon we will continue our tutorial series. The final day of the meeting will focus on the technology underlying Galaxy and biological data analysis with a focus on containerisation, software packaging for easier use and cloud deployment. Tutorials on this day will focus on similar topics.

Register now.

Galaxy Administrators Course Report

  Galaxy Administrators Course

A very successful and inspiring Galaxy admin workshop was held in Oslo in January, Thanks to 33 highly motivated participants and Nicola Soranzo, Marius Van Den Beek, Abdulrahman Azab, Björn Grüning and Enis Afgan as instructors! Thanks also to ELIXIR, de.NBI, and ELIXIR Norway for sponsoring this event.

Plenty of materials for Galaxy administration are now up to date and available online. The workshop included a sneak preview of what's coming in the 18.01 release from Nate Coraor.

Select Upcoming events

Date Topic/Event Venue/Location Contact
February 1st 2018 Galaxy-P: an accessible resource for multi-omics analysis Lorne Proteomics Symposium, Lorne, Victoria, Australia Maria Doyle
February 6th 2018 Bioinformatic Analysis of Next Generation Sequencing Data National Institutes of Health (NIH), Bethesda, Maryland, United States training@faes.org
February 7th 2018 An Introduction to Integrative Bioinformatics and Novel Tools in Multi-Omics CPSA Europe, Cambridge, United Kingdom Stephan Kang
February 12th 2018 Supporting Highly Scalable Scientific Data Analysis with Galaxy Converged IT & the Cloud, San Francisco, California, United States James Taylor
February 17th 2018 Open Source Breakthroughs in Life Sciences and Precision Medicine Open Source 101 - Raleigh, North Carolina, United States Stephan Kang
February 21st 2018 RNA Sequencing and Differential Expression University of Aberdeen, Scotland, United Kingdom Training offered by GTN MemberSophie Shaw
February 26th 2018 5th Galaxy high-throughput sequencing (HTS) data analysis workshop University of Freiburg, Freiburg Germany Training offered by GTN MemberFreiburg Galaxy Team
March 7th 2018 Introduction to RNA-Seq data analysis with Galaxy Am Botanischen Garten, Kiel, Germany Training offered by GTN MemberAndrea Bagnacani, Markus Wolfien
March 14th 2018 Galaxy community kickoff meeting and Galaxy User Conference Freiburg, Germany ELIXIR Galaxy Working Group
March 20th 2018 RNA-Seq Differential Gene Expression Analysis using Galaxy and the GVL Melbourne Bioinformatics, Carlton, Victoria, Australia Training offered by GTN MemberChristina Hall
March 20th 2018 Introduction to Galaxy and the GVL Melbourne Bioinformatics, Carlton, Victoria, Australia Training offered by GTN MemberChristina Hall
March 21st 2018 Variant Calling with Galaxy & the GVL for beginners Melbourne Bioinformatics, Carlton, Victoria, Australia Training offered by GTN MemberChristina Hall
March 21st 2018 Alignment, Visualisation and Variant Calling University of Aberdeen, Scotland, United Kingdom Training offered by GTN MemberSophie Shaw
April 3rd 2018 Galaxy Africa SANBI, University of the Western Cape, Cape Town, South Africa Training offered by GTN Membergalaxyafrica@sanbi.ac.za
April 10th 2018 Galaxy : Traitement de données de séquences par Galaxy AGROCAMPUS OUEST, Campus de Rennes, France Training offered by GTN MemberYvan Le Bras, Sandrine LAGARRIGUE, formco@agrocampus-ouest.fr
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
May 14th 2018 Science Gateways Bootcamp TACC, Austin, Texas, United States help@sciencegateways.org
May 21st 2018 Big Genomics Data Skills Training course JAX Genomic Medicine, Farmington, Connecticut, United States Charlie Wray
June 25th 2018 GCC2018 & BOSC 2018 Reed College, Portland, Oregon, United States Training offered by GTN MemberOrganizers

New Galactic Blog Entry: Galaxy R Markdown Tools

Galactic Blog

January saw one new Galactic Blog entry:

Galaxy Cloud News

January was a big month for Galaxy in the cloud:

Publications

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

Highlighted Publications

The Galactic and Stellar publications added in January were:

Publication Topics

# Tag # Tag # Tag # Tag
67 +Methods 30 +Workbench 22 +UsePublic 10 +UseMain
8 +UseLocal 4 +Reproducibility 4 +IsGalaxy 3 +RefPublic
3 +Tools 3 +Shared 2 +Other 1 +Visualization
1 +HowTo 1 +Unknown

Who's Hiring

Please Help! Yes you!

The Galaxy is expanding! Please help it grow.

Have 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 last month, including two new public servers:

A-Game

A-Game

A-Game is A Galaxy suite for tArgeted MEtagenomics, a web service incorporating state of the art tools and workflows for the analysis of eDNA sequence data. A site manual and example workflows are available.

A-Game is supported by BEACON at the Dipartimento di Bioscienze, University of Milan

Splicescope

Splicescope

Splicescope is a tool-publishing server for predicting neuronal maturation using splicing profiles. Splicescope takes either an exon inclusion ratio matrix file or junction bed files from multiple samples as input and outputs a zip file including prediction results, PCA analysis results and a PCA plot based on reference samples and an html file to summarize the prediction.

Splicescope can be accessed anonymously, or with an account, and anyone can create an account. It is supported by the Zhang Laboratory, Department of Systems Biology, the Department of Biochemistry and Molecular Biophysics, and the Motor Neuron Center at Columbia University Medical Center.

New video from the Galaxy-P team

Public Servers in Publications

We tag papers that use, mention, implement or extend public Galaxy Servers. Here are the counts for January's publications.

# Tag # Tag # Tag # Tag
12 >Huttenhower 3 >Workflow4Metabolomics 1 >GVL-Unspecified 1 >Galaxy-P
1 >Osiris 1 >PreSTIGE 1 >PIA 1 >Splicescope
1 >A-Game 1 >Cistrome 1 >Orione 1 >GVL-QLD
1 >RepeatExplorer

Tools

ToolShed Contributions

Galaxy ToolShed

Tool Shed contributions in January.

Releases

Earlier Releases

17.09 Galaxy Release

GalaxyProject

The Galaxy Committers published the 17.09 release of Galaxy at the end of October.

Highlights include

  • Singularity Tool execution using the HPC-friendly container technology Singularity is now supported.
  • Download entire collection Downloading whole collections is now possible from the history interface. (Thanks to @mvdbeek.)
  • Switch tool versions in workflows You can now select exactly what version of tool you want to use when building workflows. (Thanks to @mvdbeek.)
  • Security patches
  • Several features were deprecated

See the 17.09 release announcement for details.

Galaxy Docker Image 17.09

The Galaxy Docker project has seen a matching release, for Galaxy 17.05. Major features include

  • much improved documentation about using Galaxy Docker and an external cluster (@rhpvorderman)
  • CVMFS support - mounting in 4TB of pre-build reference data (@chambm)
  • Singularity support and tests (compose only)
  • more work on K8s support and testing (@jmchilton)
  • using .env files to configure the compose setup for SLURM, Condor, K8s, SLURM-Singularity, Condor-Docker

And

ephemeris 0.8.0

Ephemeris is a small Python library and set of scripts for managing the bootstrapping of Galaxy plugins - tools, index data, and workflows.

blend4php 0.1 beta

blend4php

The beta version of the blend4php package, a PHP wrapper for the Galaxy API, was released in December. It provides a PHP package for interacting with Galaxy and CloudMan. blend4php currently offers a partial implementation of the Galaxy API and includes support for datasets, data types, folder contents, folders, genomes, group roles, groups, group users, histories, history contents, jobs, libraries, library contents, requests, roles, search, tools, toolshed repositories, users, visualizations and workflows.

The motivation for development of this library is for integration with Tripal, an open-source toolkit for creation of online genomic, genetic and biological databases.

Please see the API documentation page for full information.

galaxy-lib 17.9.10

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 revision:

  • Added docs for using mulled-build with your own quay.io account (thanks to @jerowe).
  • Catch errors in Conda search if nothing is found (preventing planemo-monitor from functioning properly) (thanks to @bgruening).
  • Make multi-requirement container building via mulled more stable (thanks to @bgruening).

Planemo 0.47.0

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.

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

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.

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).

And the rest ...

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

Other News