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July 2014 Galaxy Update

Galaxy Updates

Welcome to the July 2014 Galaxy Update, a monthly summary of what is going on in the Galaxy community. Galaxy Updates complement the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.  

The Galaxy Update is going out a few days early this month because the usual release date is during GCC2014.


GCC2014: June 30 - July 2

GCC2014: June 30 - July 2, Baltimore

The 2014 Galaxy Community Conference (GCC2014) starts on Monday, June 30, and runs through July 2, at the Homewood Campus of Johns Hopkins University, in Baltimore, Maryland, United States. The program is online and all titles and abstracts for accepted talks and posters are now online.

Fifteen Training sessions on 12 topics, several Birds of a Feather, two lightning talk sessions, and the very first Galaxy Project Hackathon are also happening.

Galaxy @ ISBMB and BOSC 2014

BOSC 2014    ISMB 2014

There will be at least six talks and five posters related to Galaxy at ISMB and BOSC 2014 this year. Talks include

Other Events

Over the rest of the summer there are other Galaxy related events in Leiden, Sydney, Brisbane, São Paulo, and Rio de Janeiro. Also see the Galaxy Events Google Calendar for details on other events of interest to the community.





June 28-30

Galaxy Hackathon

Homewood Campus of Johns Hopkins University, Baltimore, Maryland, United States


June 30 -
July 2

2014 Galaxy Community Conference (GCC2014)


July 7-9

NBIC/BioSB RNA- seq data analysis course

Leiden, the Netherlands

NBIC/BioSB <education AT biosb DOT nl>

July 10

An Introduction to Galaxy with the Genomics Virtual Lab

Post-GSA 2014 Workshop, Sydney, Australia

Mark Crowe

July 11-15

ISMB and BOSC 2014

At least six talks and five posters

Boston, Massachussetts, United States

See presenter list

July 18

Workshop: RNA-Seq analysis using Galaxy

Brisbane, Australia

Mark Crowe

July 28 - August 1

Workshop: DNA Sequence Bioinformatics Analysis with the Galaxy Platform

University of São Paulo (USP), São Paulo, Brazil

Dave Clements

August 25-27

Análise e anotação funcional de seqüências NGS usando Stingray@Galaxy

Fiocruz, Rio de Janeiro, Brasil

Plataforma de Bioinformática do IOC <>

September 6-10

T07 - Scientific Workflows for Analysing, Integrating and Scaling Bioinformatics Data: a Practical Introduction to Galaxy, Taverna and WS-PGRADE

European Conference on Computational Biology (ECCB'14), Strasbourg, France

Hailiang (Leon) Mei

September 30 - October 2

RNA-Seq & ChIP-Seq analysis course using Galaxy

PRABI, Lyon, France

Navratil V <navratil AT prabi DOT fr>., Oger C. <oger AT prabi DOT fr>, Veber P. <veber AT prabi DOT fr>, Deschamps C. <deschamps AT prabi DOT fr>, Perriere G. <perriere AT prabi DOT fr>

September 30 - October 2

Galaxy Training and Demo Day

Bern (Switzerland)

Hans-Rudolf Hotz and Bjoern Gruening

(second Swiss) Galaxy Workshop

SyBIT Tech Day, Bern (Switzerland)

German Galaxy Developers Day

Freiburg (Germany)

New Papers

48 papers were added to the Galaxy CiteULike Group in June. Some papers that may be particularly interesting to the Galaxy community:

The new papers were tagged in many different areas:










































Who's Hiring

Please Help! Yes you!

The Galaxy is expanding! Please help it grow.

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

New Public Servers

One new public Galaxy server was added to the published list in June:


Genomics Virtual Lab

Galaxy Distributions

June 2, 2014 Galaxy Distribution

Dataset Collections Workflow Detail
example dataset collection workflow (credits)

News Brief Highlights:

  • Dataset Collections introduced
  • Changes to database build (dbkey) organization
  • Enhancements to Tool configuration and Workflow options
  • Trackster, User Interface, and Admin panel upgrades
  • Significant updates to Admin and Job functionality
  • Tool Shed repository and API additions
  • Data updates plus new Security features and Bug fixes



$ hg clone 


$ hg pull 
$ hg update latest_2014.06.02

Tool Shed June 2, 2014 Release

A corresponding version of the ToolShed was also released on June 2, 2014. Highlights include

BioBlend and CloudMan

BioBlend 0.4.3 was released on April 11, 2014.

The most recent version of CloudMan was released in January 2014.

Galaxy Community Hubs

   Galaxy Community Log Board
Galaxy Deployment Catalog   

   Share your experience now   
Describe your instance now

One new Log Board entry was added in June:

The Community Log Board and Deployment Catalog Galaxy community hubs were launched last your. If you have a Galaxy deployment, or experience you want to share then please publish them.

Galaxy ToolShed

ToolShed Contributions

Galaxy Project ToolShed Repos

In no particular order:


  • From qfab

    • pynast: PyNAST is a sequence aligner for adding new 16S rDNA sequences to existing 16S rDNA alignments - GVL

    • fasttree_linux_64bit: FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL

    • rarefaction: Rarefaction calculation based on mothur's rarefaction.single command - GVL

  • From crs4

  • From evan

    • bwa_wrappers: Galaxy wrappers for the BWA short read aligner.

  • From anton

  • From superyuan

    • refeditor: Produces a personalized diploid reference genome based on all known genetic variants of that particular individual.

  • From iracooke

    • make_protein_decoys: Generate a decoy database from an input set of protein sequences. Decoys generated using this tool can be used for tandem ms searches.

    • proteindb_from_gff3: Convert Augustus Generated gff3 to a Protein Database

    • protxml_to_gff: Map peptides from a protXML file to genomic coordinates

    • sixframe_translate: Translates sequences in a nucleotide fasta file to protein

  • From hyungrolee

    • mgescan: MGEScan: Identifying long terminal repeats (LTR) and non-LTR retroelements in eukaryotic genomic sequences.

  • From iuc

    • samtools_sort: Sort alignments by leftmost coordinates or read name.

  • From devteam

    • bamleftalign: utility for leftaligning indels in BAM datasets. Based on bamleftalign utility for FreeBayes package.

Packages / Tool Dependency Definitions

Tool Updates:

Other News