October 2017 Galaxy News

Galaxy News

Welcome to the October 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.


Hacktoberfest

What do fall foliage, pumpkin beer, and Halloween have in common? October! Or, we should say Hacktoberfest. From Oct 1st through Oct 31st, Hacktoberfest is a celebration of open source coding organized by Digital Ocean and GitHub. This is a great opportunity to get involved with a project and get some help along the way. Plus, if you issue 4 pull request during the month, you get a limited edition t-shirt! Any project on GitHub can participate simply by creating and tagging issues with Hacktoberfest tag. If you'd like to participate on a Galaxy-related project, see the Galaxy Hacktoberfest dashboard.

The Galaxy Publication Library has moved to Zotero.

Galaxy Publication Library at Zotero

After residing on CiteULike since 2011, the Galaxy Publication Library has moved to Zotero. See the announcement for full details.

Highlighted Publications

With the move to Zotero, we added two tags to highlight papers that either emphasize Galaxy ("+Stellar"), or are about Galaxy ("+Galactic"):

The Galactic and Stellar publications added in September were:

Publication Topics

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

# Tag # Tag # Tag # Tag
58 +Methods 23 +Workbench 21 +UsePublic 11 +UseLocal
10 +UseMain 10 +RefPublic 8 +Tools 6 +IsGalaxy
5 +Reproducibility 3 +Shared 1 +Other 1 +Cloud
1 +Unknown

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


Upcoming events

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

DateTopic/EventVenue/LocationContact
October 3rd 2017 Introduction to Galaxy & the Genomics Virtual Laboratory Melbourne Bioinformatics, Carlton, Victoria, Australia Training offered by GTN Memberenquiries@ melbournebioinformatics.org.au
October 4th 2017 RNA-Seq Differential Gene Expression Analysis using Galaxy & the GVL Melbourne Bioinformatics, Carlton, Victoria, Australia Training offered by GTN Memberenquiries@ melbournebioinformatics.org.au
October 4th 2017 Introduction to Galaxy & the Genomics Virtual Laboratory Melbourne Bioinformatics, Carlton, Victoria, Australia Training offered by GTN Memberenquiries@ melbournebioinformatics.org.au
October 4th 2017 A primer for RNA-Seq processing, interpreting and visualization University of Freiburg, Freiburg Germany Steve Hoffmann, Olaf Wolkenhauer, Wolfgang Hess
October 5th 2017 Variant Calling with Galaxy & the GVL for beginners Melbourne Bioinformatics, Carlton, Victoria, Australia Training offered by GTN Memberenquiries@ melbournebioinformatics.org.au
October 18th 2017 SACNAS 2017 Pre-Conference Workshops 2017 SACNAS, Salt Lake City, Utah, United States Training offered by GTN MemberCamille Avestruz, Amanda Cooksey, 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 Training offered by GTN MemberCamille Avestruz, Tracy Teal, Joslynn Lee, Dave Clements
October 23rd 2017 RNA Bioinformatics and Galaxy The Future Development of Bioinformatics in Germany and Europe, ZiF, Bielefeld University, Bielefeld, Germany Rolf Backofen, Björn Grüning
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
November 1st 2017 Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter Genome Informatics, CSHL, New York, United States Training offered by GTN MemberAnton Nekrutenko
November 1st 2017 Hybrid assembly of small genomes in Galaxy Genome Informatics, CSHL, New York, United States Training offered by GTN MemberDelphine Lariviere
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 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
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 September.

Public Servers in September's Publications

As mentioned above, 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 September's papers.

# Server # Server # Server # Server
14 >Huttenhower 5 >RepeatExplorer 4 >Workflow4Metabolomics 3 >RiboGalaxy
2 >GVL-QLD 1 >PreSTIGE 1 >BioCiphers 1 >PhenoMeNal
1 >Galaxy-P 1 >Codon Harmonizer

Public Server Directory Rebuilt

The public Galaxy server directory was rebuilt in September to take advantage of Hub support for such directories. Take a look.

ImmPort Galaxy: New Release and Feedback Needed

ImmPort Galaxy

The ImmPort Project just released a new version of ImmPort Galaxy. You can now upload your flow data as flowFrames, and there are new tools too:

  • Edit marker or channel names in FCS files – fix any typo to make your FCS files compatible for multi-files analysis
  • Merge and downsamples FCS files – create an aggregate of your files to identify patterns or populations in your sample set.
  • Generate a Self-Organizing Map using FlowSOM,
  • Compare individual files to the tree, or
  • Compare samples to one another using the FlowSOM tree.
  • Visualize your data with an interactive heatmap generated by Clustergrammer.

The ImmPort Project is also seeking feedback on how people use the ImmPort Galaxy server. If you are a user then please let them know. (And if you aren't a user and you do flow cytomety then give ImmPort Galaxy a look.)

Codon Harmonizer

Wageningen UR

Codon Harmonizer supports generating codon harmonized variants of gene sequences for heterologous expression. This tool-publishing server comes from the Laboratory of Microbiology at Wageningen University and Research

From Claassens et al.:

"...different codon usage variants significantly improved production of some of the tested proteins. However, not a single algorithm performed consistently best for the membrane-integrated production of the 6 tested proteins. In conclusion, for improving heterologous membrane protein production in E. coli, the major effect is accomplished by transcriptional tuning. In addition, further improvements may be realized by attempting different codon usage variants, such as codon harmonized variants, which can now be easily generated through our online Codon Harmonizer tool."

A manual and email support (Bart Nijsse, Nico Claassens) are available.

See the Codon Harmonizer page for more.


Tools

ToolShed Contributions

Galaxy ToolShed

Tool Shed contributions in September.

Releases

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.

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).

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.

sequence_utils 1.1.1

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

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.

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)

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

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, visit 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