August 2012 Galaxy Update

Galaxy Updates

Welcome to the August 2012 edition of 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.

New Papers

These papers may be of interest to the Galaxy community:

These papers were among 29 papers added to the Galaxy CiteULike group since the last Galaxy Update (for a total of 375 papers in the last ~18 months). The new papers are spread across 6 categories.

GCC2012 & GCC2013

2012 Galaxy Community Conference       

2013 Galaxy Community Conference

The [2012 Galaxy Community Conference (GCC2012)](/events/gcc2012/) was held July 25-27, in Chicago. Highlights included:

Slides for most talks are already on the wiki, and the rest will trickle in over the next week. Videos of talks and workshops will be posted in about two weeks. Finally, with over 200 registrations, this was for the third year running, the largest Galaxy conference yet.

GCC2013 was also announced at the meeting. It will be held 30 June through 2 July in Oslo, Norway. Watch the GCC2013 page for information as it become available.

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.

Upcoming Events and Deadlines

Bioinformatics Short Course: Mutation Detection Using Massively Parallel Sequencing: From Data Generation to Variant Annotation 2012 GMOD Summer School South African Genetics and Bioinformatics Society Conference Swiss Galaxy Day


There are August application, poster, and paper deadlines for

August events including a Bioinformatics Short Course on Mutation Detection at the University of Iowa, and the [2012 GMOD Summer School]( GMOD Summer School).

See the Galaxy Events Google Calendar for details on these and other events.


Date Topic/Event Venue/Location Contact
August 1-3 Bioinformatics Short Course: Mutation Detection Using Massively Parallel Sequencing: From Data Generation to Variant Annotation University of Iowa, Iowa City, United States Iowa Initiative in Human Genetics
August 25-29 GMOD Summer School US National Evolutionary Synthesis Center (NESCent), Durham, North Carolina, United States Dave Clements
September 3-4 Galaxy Workshop University of Pretoria, Pretoria, South Africa Dave Clements
September 6-7 Stellenbosch University, Stellenbosch, South Africa
September 10-11 Systems Bioinformatics Workshop Institute for Systems Biology
Seattle, Washington, United States
James Taylor
September 10-12 Transparent, accessible, reproducible analysis with Galaxy South African Genetics & Bioinformatics Society Conference
University of Stellenbosch, Stellenbosch, South Africa
Dave Clements
September 27-29 Beyond the Genome 2012 Harvard Medical School, Boston, Massachusetts James Taylor
October 3 (first Swiss) Galaxy Workshop SyBIT Tech Day, Bern, Switzerland Hans-Rudolf Hotz
October 8-12 Extending High-Performance Computing Beyond its Traditional User Communities Workshop 8th IEEE International Conference on eScience (eScience 2012), Chicago Illinois, United States James Taylor

Swiss Galaxy Day

Swiss Galaxy Day

The 1st Swiss Galaxy Workshop will be held October 3-4 in Bern, and is aimed at Galaxy administrators and users alike. We also welcome participants who are using other workflow management systems, and tool developers who are looking for such systems to offer their tools to a wider audience.

We would like to discuss the status of the Galaxy project, new developments, interface to other systems, extensions and best practice in reproducible research.

The workshop is part of the SyBIT Tech Day series.

Tool Shed Contributions

Several new repositories were added to the Galaxy Tool Shed in July.

  • nosql_interface query and download data from MongoDB and CouchDB NoSQL databases
  • synapse_interface interface with Sage Bionetworks Synapse platform
  • mtls_analysis: Analyze and compare multiple ChIP-seq experiments
  • trinityrnaseq: De novo assembly of rna-seq data coupled with downstream analyses
  • Toolfactory: Turn scripts into Galaxy Tools; presented at GCC2012
  • protk: Identify Peptides and Proteins from tandem Mass Spec data; also presented at GCC2012
  • deseq_and_sam2counts: RNA-Seq differential expression analysis on aligned reads to a transcriptome using sam2counts and DESeq; also presented at GCC2012
  • freebayes: Bayesian genetic variant detection tool
  • GFAP: annotate & prioritize human genetic variants identified by NGS

New Distributions

A new Galaxy distribution was released on July 20, 2012. Highlights include:

  • Freebayes has moved from the Galaxy distribution to the Galaxy's Main Tool Shed
  • EMBOSS version 5.0.0 tool dependencies in the emboss_5 repository of the Galaxy Main Tool Shed updated to include information for automatically installing.
  • Tool Shed now also supports specifying the third party tool dependencies to be automatically installed in new repositories
  • Admin Genome Indexing is now in BETA. Download, index, and track progress right from the admin UI! That's a screen shot on the right ->
  • Improved Error Handling that captures EXIT codes, STDOUT, and STDERR from tools in XML. Be sure to read full details.
  • TopHat2/Bowtie2 latest support includes option to 'report discordant pairs', updated tests, and more preset options.
  • Trackster new parameter space visualization. BRAND NEW!! More details coming soon, but give a test drive now.

Other News