March 2018 Galaxy News

Galaxy News

Welcome to the March 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.


GCCBOSC 2018

GCCBOSC 2018

Abstract submission, registration & housing are open

We are pleased to announce that abstract submission and early registration for GCCBOSC2018 are now open.

GCCBOSC 2018 will be held 25-30 June in Portland, Oregon, United States. This brings the 2018 Galaxy Community Conference and the Bioinformatics Open Source Conference together into a unified week-long event. If you work in open source life science or data-intensive biomedical research, then there is no better place than GCCBOSC 2018 to present your work and to learn from others.

GCCBOSC starts with two days of training with a wide range of topics nominated and selected by our communities. Training is followed by a two day meeting, with joint and parallel tracks, featuring oral presentations, posters, demos, lightning talks, birds-of-a-feather and invited keynotes. The week finishes with CollaborationFest Core and Encore, two or four days of collaborative work on code, documentation, training and challenging data analysis problems.

Training schedule set

A big thank you to everyone who nominated topics, voted on topics, helped create workshop descriptions, and to the instructors who will be presenting in June. All your efforts and input have helped us create two full days of training at GCCBOSC.

The first day has two tracks about Galaxy, each with three sessions:

  • Intro to Using Galaxy
  • Intro to Galaxy Administration

The second day has five parallel track, and covers a full spectrum of topics of interest to those working in and with open source bioinformatics:

Keynote speakers

We are pleased to announce two of our keynote speakers:

Fernando Pérez

BOSC / GCC Joint Keynote: Fernando Pérez

Dr. Pérez is an assistant professor in Statistics at UC Berkeley and a Faculty Scientist in the Department of Data Science and Technology at Lawrence Berkeley National Laboratory. He also created IPython while a graduate student and co-founded its successor, Project Jupyter.

Tracy Teal

BOSC 2018 Keynote: Tracy K. Teal

Dr. Teal is the Executive Director of The Carpentries. She co-founded Data Carpentry to develop and scale this training, and Data Carpentry has now joined with Software Carpentry to form The Carpentries and more broadly meet training and community needs.

GCCBOSC 2018 Sponsors

We are happy to have several confirmed GCCBOSC 2018 sponsors. This month we are highlighting F1000Research and the Technology Association of Oregon:

F1000Research

F1000Research

For the first time, the Galaxy Community Conference and Bioinformatics Open Source Conference are joining together for a unified event. To mark this occasion, the BOSC Collection and the Galaxy Gateway on F1000Research will be publishing a series of articles in the run up to the conference in June and are now inviting contributions. The submission deadline is April 30th, to ensure papers are published before GCCBOSC 2018 starts. If you are interested in contributing or have any other questions, please email research@f1000.com.

Technology Association of Oregon

Technology Association of Oregon is the force behind the Oregon tech industry. Supporting entrepreneurs, connecting peers and decision makers, and helping grow the Northwest as a global hub for innovation. We are proud to be a leader in the regional technology community and offer many ways for individuals, companies, and community organizations to partner with us in Oregon and SW Washington.


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 community, 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, 3-5 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.

The inaugural Galaxy Africa meeting represents the start of building a data intensive analytics network in Africa. This annual meeting is intended be the networking space for bioinformatics and system administrators to strengthen tool development and research.

Register now.

Conference Fellowships

If you would like to attend, but need financial assistance to get there, then you are encouraged to apply for a conference fellowship. Fellowship application review will start 10 March. Fellowships are provided by the Galaxy Community Fund.

Upcoming events

These and other Galaxy related events coming up in the next few months:

DateTopic/EventVenue/LocationContact
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 Alignment, Visualisation and Variant Calling University of Aberdeen, Scotland, United Kingdom Training offered by GTN MemberSophie Shaw
March 21st 2018 Variant Calling with Galaxy & the GVL for beginners Melbourne Bioinformatics, Carlton, Victoria, Australia Training offered by GTN MemberChristina Hall
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
April 23rd 2018 4th de.NBI Genomics training course Justus-Liebig-Universität, Gießen, Freiburg Germany denbi_genomics @ computational.bio
May 14th 2018 Formation metabarcoding 2018 Station Biologique de Roscoff, France Training offered by GTN MemberIntervenants
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
May 29th 2018 Bioinformatique - Analyse avancée de séquences Bordeaux, France Intervenants
June 12th 2018 G-OnRamp Workshop Washington University in St. Louis, Missouri, United States Training offered by GTN MemberJeremy Goecks, Sarah Elgin
June 25th 2018 GCCBOSC 2018 Reed College, Portland, Oregon, United States Training offered by GTN MemberOrganizers
July 16th 2018 G-OnRamp Workshop Washington University in St. Louis, Missouri, United States Training offered by GTN MemberJeremy Goecks, Sarah Elgin

New Galactic Blog Entry: Coding in the Winter Wonderland: Galaxy Admin Training

Galactic Blog

February had one new Galactic Blog entry:

Publications

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

Highlighted Publications

The Galactic and Stellar publications added in February were:

Publication Topics

# Tag # Tag # Tag # Tag
93 +Methods 37 +UsePublic 21 +Workbench 20 +UseMain
12 +RefPublic 12 +UseLocal 4 +Shared 4 +Tools
4 +Reproducibility 2 +HowTo 2 +Cloud 2 +IsGalaxy
1 +Visualization 1 +UseCloud

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 a new public server:

Metaproteomics Gateway Server

Metaproteomics Gateway Server

The Galaxy-P Metaproteomics Gateway provides access to documentation and other instructional materials, and an opportunity for hands-on training using example datasets and optimized metaproteomics workflows. The main goal of this server is to provide documentation to facilitate training and mastery of these software and workflows.

Step-by-step training instructions and related information and a Metaproteomics Tutorial Video are available. The server can be accessed anonymously or you can create an account. It is maintained by @galaxyproteomics.

See Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework by Clemens Blank et al. for more.

deepTools 3.0 is live

deepTools 3.0 is now available on the deepTools Galaxy Server. Changes include a completely revamped normalization interface (and new methods), CRAM support, interactive plots, a more homogenized interface, new tools and better MultiQC integration

ARGs-OAP v2.0 published

In addition to being referenced in several papers last month (see below), the ARGs-OAP server was upgraded as well:

Public Servers in Publications

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

# Tag # Tag # Tag # Tag
15 >Huttenhower 7 >RepeatExplorer 6 >ARGs-OAP 3 >Workflow4Metabolomics
3 >Orione 2 >Cistrome 2 >Galaxy-P 2 >RNA-Rocket
1 >PhenoMeNal 1 >Osiris 1 >BioCiphers 1 >Metaproteomics Gateway
1 >Mississippi 1 >BIPAA 1 >Genomic Hyperbrowser 1 >RiboGalaxy
1 >APOSTL 1 >PreSTIGE 1 >GenAP 1 >GVL-Unspecified
1 >Pasteur 1 >GalaxEast

Tools

ToolShed Contributions

Galaxy ToolShed

Tool Shed contributions in February.

Releases

Planemo 0.48.0

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.

Pulsar 0.8.1-3

Pulsar

Pulsar updates were released in February. 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.

galaxy-lib 17.9.11-18.5.2

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.

Earlier Releases

Other packages released in the prior 4 months.

17.09 Galaxy Release

GalaxyProject

The Galaxy Committers published the 17.09 release of Galaxy in 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.

And the rest ...

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

Other News