August 2013 Galaxy Update

Galaxy Updates

Welcome to the August 2013 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.


2013 Galaxy Community Conference (GCC2013)

GCC2013 Report

The 2013 Galaxy Community Conference (GCC2013) was held a month ago in Oslo Norway, at the University of Oslo. Video of all accepted talks, the slides for most accepted and lightning talks, handouts and slides for all Training Day sessions, and most posters are now available online.

GCC2013 was, by all accounts, a tremendous success. This was the largest GCC ever held, and featured poster sessions and Birds of a Feather gatherings for the first time. The evening gatherings at the pub and the conference dinner at the historic Sporten venue, high above Oslo, also proved quite popular.

In addition to the videos and presentation materials, there are also several meeting reports in a wide variety of presentation styles:


New Public Servers

Two new servers joined the list of over 30 publicly accessible Galaxy servers in July.

PredPharmTox

PredPharmTox

PredPharmTox implements the QuantMap tools for grouping chemicals by biological activity. See "Automated QuantMap for rapid quantitative molecular network topology analysis" by Schaal1, et al., Bioinformatics (2013), for more.

QBRC Galaxy

QBRC Galaxy

The QBRC Galaxy Server hosts custom tools developed by members of the Quantitative Biomedical Research Center @ University of Texas Southwestern for statistical analysis of various High Throughput Sequencing experiments.

Features

The QBRC galaxy server tools are constantly being updated. Please contact authors for more details regarding use.

New Papers

# Tag    # Tag    # Tag
22 methods 4 cloud 1 Project
15 workbench 3 usepublic 1 reproducibility
7 tools 3 uselocal 1 usecloud
7 usemain 3 shared
5 isgalaxy 2 refpublic

47 new papers were added to the Galaxy CiteULike Group in July. These papers may be particularly interesting to the Galaxy community


SlipStream Appliance: Galaxy Edition Announced

SlipStream Appliance - Galaxy Edition

BioTeam has announced the SlipStream Appliance: Galaxy Edition – "a high-performance, server class device pre-loaded with a fully operational Galaxy analysis platform." It is a plug-and-play solution, "intended to make Galaxy more accessible by relieving some of the burdens users may experience with other methods of accessing the platform." See the product page for more details.


New Galaxy Proteomics Mailing List

Galaxy Proteomics Mailing List

The Galaxy community now has a mailing list dedicated to proteomics. If you're using Galaxy to do proteomics, or if you are thinking of doing so then please subscribe. In case you missed it, there is also a proteomics wiki page.

See the complete list of mailing lists for more information on this and other Galaxy mailing lists, including links to searchable archives of all Galaxy lists.

Many thanks to Ira Cooke and John Chilton for suggesting this and taking the lead in gathering the Galaxy Proteomics 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.


Events

ISMB/ECCB 2013
BOSC 2013
MS SIG 2013: Beyond the Proteomics

ISMB / ECCB / BOSC / MS SIG 2013

Galaxy had a strong presence at ISMB / ECCB 2013, BOSC, and MS SIG in Berlin this year. Slides for 15 talks, posters, workshops related to Galaxy are now available online. Also see the summary from Bioinformatics Open Science Codefest 2013: Tools, infrastructure, standards and visualization.


Other Upcoming Events

RNA-Seq Workshop: From Pipette to P-value! @ UC Davis Bioinformatics Core The Genomic Bioinformatics Workshop Individualizing Medicine Conference   Beyond the Genome   Analisi dati Next Generation Sequencing in Galaxy: exome, RNA-Seq, metagenomica   Galaxy Training Days
See the Galaxy Events Google Calendar for details on these and other events.
Date Topic/Event Venue/Location Contact
September 9-11 RNA-Seq Workshop: From Pipette to P-value! UC Davis Bioinformatics Core Davis, California, United States Email
September 28 - October 1 Galaxy Workshop The Genomic Bioinformatics Workshop, Sydney, Australia Jennifer Jackson, Ross Lazarus
September 30 - October 2 TBA, part of the Cancer Care session Individualizing Medicine Conference, Mayo Clinic, Rochester, Minnesota, United States James Taylor
October 1-3 Galaxy Beyond the Genome 2013,San Francisco, California, United States Jeremy Goecks
October 7-8 TBD NGS & Bioinformatics Summit Europe Anton Nektutenko
Using Galaxy to Provide a NGS Analysis Platform Hans-Rudolf Hotz
October 8-11 Analisi dati Next Generation Sequencing in Galaxy: exome, RNA-Seq, metagenomica CRS4, Loc. Pixinamanna, Pula CA, Italy Paolo Uva
October 9-11 Galaxy Training Days GenoToul bioinformatics facility, INRA, Toulouse Auzeville, France Sarah Maman
October 22-26 High Throughput Data Analysis and Visualization with Galaxy ASHG 2013, Boston, Massachusetts, United States Anton Nekrutenko, Jennifer Jackson

# Galaxy Distributions The most recent official distribution was on June 3, 2013. There was a minor security patch released on June 12. ## CloudMan Release
CloudMan

A new version of CloudMan was released in July.

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.

IMPORTANT - please read

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. Note that this upgrade is a major version upgrade and thus the migration is rather complicated. The migration process has been automated but will take a little while to complete. If you have made customizations to your cluster in terms of adding file systems, upgrading the database, or similar, we do not recommend you perform the upgrade. Note that this upgrade comes with (and requires) a new AMI (ami-118bfc78), which will automatically be used when starting an instance via CloudLaunch.

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

  • Unification of galaxyTools and galaxyData file systems into a single galaxy filesystem. This change makes it possible to utilize the Galaxy Tool Shed when installing tools into Galaxy.
  • Added initial support for Hadoop-type workloads
  • Added initial support for cluster federation via HTCondor
  • Added a new file system service for an instance's transient storage, allowing it to be used across the cluster over NFS
  • Added a service for the Galaxy Reports webapp
  • Added optional Loggly based off-site logging support
  • Added tags to all resources utilized by CloudMan

For more details on the new features, see the the CHANGELOG and for even more details see, all 291 commit messages from 7 contributors.


Tool Shed Contributions

Galaxy Tool Shed
  • varscan: mutation callers for targeted, exome, & whole-genome resequencing; cancer genomics
  • jointsnvmix: Somatic mutations caller using probabilistic graphical model w/ tumour/normal pairs
  • scaffold: Tool wrapper for the commercial proteomics application Scaffold
  • trim_galore: adaptive quality and adapter trimmer
  • bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications
  • augustus: eukaryotic gene predictor
  • glimmer3: microbial DNA gene finder.
  • trna_prediction: Prediction of t-RNA with aragorn and tRNAscan-SE
  • rseqc: converts RNA-seq data from .bam to .wig
  • sickle: A windowed adaptive trimming tool for FASTQ files using quality
  • tabix: index TAB-delimited genome position file in.tab.bgz; creates an index file in.tab.bgz.tbi
  • glimmer_gene_calling_workflow: Gene calling with glimmer and trainingset of known genes.
  • vcftools: validate/merge/compare/calculate basic population genetic statistics on VCF.
  • bcftools: work with BCF data
  • cmpfastq: compare QC filtered fastq files
  • fastQValidator: validates the format of fastq files
  • bs_seeker2: Bisulfite sequencing mapper
  • spades: genome assembler for regular and single-cell projects.

Other News