December 2012 Galaxy Update

Galaxy Updates

Welcome to the December 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 37 papers added to the Galaxy CiteULike group since the last Galaxy Update.

New Public Galaxy Servers

Laboratory of Molecular Cytogenetics, Laboratory of Molecular Cytogenetics, Institute of Plant Molecular Biology

See the list of public Galaxy servers for more open and accessible Galaxy instances.

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

Plant and Animal Genome (PAG 2013) January Galaxy Admins Web Meetup ABRF 2013 2013 Galaxy Community Conference (GCC2013)

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


Date Topic/Event Venue/Location Contact
January 12-16 Galaxy Part of the GMOD Workshop at Plant and Animal Genome (PAG 2013), San Diego, California, United States Jennifer Jackson
January 16 Deploying Production Galaxy Environments on OpenStack with CloudBioLinux and CloudMan January GalaxyAdmins Web Meetup John Chilton, Srinivas Maddhi, Dave Clements
January 14-18 Ecole de bioinformatique : Initiation au traitement des données de génomique obtenues par séquençage à haut débit Station Biologique de Roscoff, France ecole-bioinfo AT aviesan DOT fr
January 28 - February 1 Phylotastic Hackathon Tucson, Arizona, United States Arlin Stoltzfus
March 2-5 SW1: Application of NGS Platforms for Whole Transcriptome and Genome Analysis and
W6: Community Resource Solutions to Analyzing Large Genomic Data Sets
ABRF 2013
Palm Springs, California, United States
Dave Clements
April 5-6 2013 GMOD Meeting Cambridge, United Kingdom, immediately prior to Biocuration 2013 Dave Clements
April 7-10 GO Galaxy Workshop Biocuration 2013, Cambridge, United Kingdom Dave Clements, Suzanna Lewis
June 30 - July 2 2013 Galaxy Community Conference (GCC2013) University of Oslo, Oslo, Norway Galaxy Outreach


We only know of one deadline coming up in December:

However, there are a few high-profile meetings:

Source Code Documentation

Galaxy-Dist at ReadTheDocs
Read the DocsSphinx Python Documentation Generator

The Galaxy Project is now using Sphinx hosted at Read the Docs to document the Galaxy code base. Two versions are available:

  • galaxy-dist: Code documentation for latest official release of Galaxy.
  • galaxy-central: Code documentation for the latest committed version of the code. This should never lag behind the Bitbucket checkins by more than an hour.

This documentation is a work in program and should make incremental improvements with each release.

New Galaxy Distributions

November 11, 2012

**Highlights:** * **NGS: Picard (beta)** tools have moved from the **[Galaxy distribution](** to the **[Galaxy Main Tool Shed](**. * The **[Intergalactic Utilities Commission](** will soon begin reviewing repositories in the **[Galaxy Main Tool Shed](** (better repos, better tools) * **[Tool Shed](** **"best practice"** advice: [a single tool or a suite of tools per repository?]( * **[Tophat](**, **[Tophat2](**, and **[Cuffdiff](** **updated** to accept gene annotations in **[GFF3](** format. * Multiple **enhancements** to the **[API](/archive/dev-news-briefs/2012-11-14/#api)** targeting user and history actions. * Plus **updates to** **[CloudLaunch](**, new **[Security Fixes](/archive/dev-news-briefs/2012-11-14/#security-fixes)**, and several usability enhancements for **Datasets**, **Datatypes**, **Tools**, and **Tool Shed** functions.
new:     $ hg clone galaxy-dist
upgrade: $ hg pull -u -r 5dcbbdfe1087

New Galaxy CloudMan Release

CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration.

This update brings a large number of updates and new features, the most prominent ones being:

  • Support for Eucalyptus cloud middleware. Thanks to Alex Richter. Also, CloudMan can now run on the HPcloud in basic mode (note that there is no public image available on the HPcloud at the moment and one would thus need to be built by you).
  • Added a new file system management interface on the CloudMan Admin page, allowing control and providing insight into each available file system
  • Added quite a few new user data options. See the UserData page for details. Thanks to John Chilton.
  • Galaxy can now be run in multi-process mode. Thanks to John Chilton.
  • Added Galaxy Reports app as a CloudMan service. Thanks to John Chilton.
  • Introduced a new format for cluster configuration persistence, allowing more flexibility in how services are maintained
  • Added a new file system service for instance's transient storage, allowing it to be used across the cluster over NFS. The file system is available at /mnt/transient_nfs just know that any data stored there will not be preserved after a cluster is terminated.
  • Support for Ubuntu 12.10
  • Worker instances are now also SGE submit hosts

This update comes as a result of 175 code changesets; for a complete list of changes, see the commit messages.

Any new cluster will automatically start using this version of CloudMan. Existing clusters will be given an option to do an automatic update once the main interface page is refreshed.

Tool Shed Contributions

Several new repositories were added to, and existing repositories updated in the Galaxy Tool Shed in the past month.

  • bsmap: A short read mapping tool for bisulfite sequencing reads
  • bowtie_wrappers, bowtie_color_wrappers, lastz, lastz_paired_ends: Wrappers all created by the Galaxy Team
  • semweb_tools: A collection of Semantic Web tools, including a (pure python) SPARQL-to-tabular format tool
  • ea_utils: FASTQ processing utilities; sam-stats added
  • regex_replace: Regular expression replacement using the Python
  • blast_datatypes and ncbi_blast_plus: Added BLAST database support
  • homer: motif discovery and next generation sequencing analysis
  • meme_chip: Motif based sequence analysis
  • SVDetect: detect genomic structural variations from paired-end and mate-pair sequencing data
  • cloudmap_in_silico_complementation: Perform in silico complementation analysis on multiple tabular snpEff output files
  • sniploid: compares SNP detected from a polyploid to those derived from its parental genomes
  • tabular_label_convert: Takes a tabular format file of numerical values and converts the labels of the rows or columns using an alias map
  • tabular_edit: Edit the contents and row/column labels of a tabular file using python statements

Other News

2013 Galaxy Community Conference (GCC2013)
2013 Galaxy Community Conference (GCC2013) Training Day