October 2012 Galaxy Update
Welcome to the October 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.
These papers may be of interest to the Galaxy community:
Some Phenotype Association Tools in Galaxy: Looking for Disease SNPs in a Full Genome, by Belinda M. Giardine, Cathy Riemer, Richard Burhans, Aakrosh Ratan, Webb Miller; in Current Protocols in Bioinformatics 39:15.2.1-15.2.27
Galaxy Workflow Integration on Garuda Grid, by K. Karuna, N. Mangala, C. Janaki, S. Shashi, and C. Subrata; in Enabling Technologies: Infrastructure for Collaborative Enterprises (WETICE), 2012 IEEE 21st International Workshop on (June 2012), pp. 194-196
The CUHK-BGI Innovation Institution of Trans-Omics (CBIIT) has now made its Galaxy server publicly available. The CBIIT Galaxy Server has the standard Galaxy tool set plus SOAPdenovo and SOAPsnp for de novo assembly and SNP calling.
There are October application, poster, and paper deadlines for
October events include the (first Swiss) Galaxy Workshop; InCoB 2012; IEEE Conference on eScience (eScience 2012, which includes the Extending High-Performance Computing Beyond its Traditional User Communities workshop); Bio-IT World Europe; BioVis: IEEE Symposium on Biological Data Visualization; Advanced NGS Course: RNA-seq data analysis (NBIC); Advanced Sequencing Technologies & Applications Course (CSHL); the Northeast and Midwest Core directors meetings; and eResearch Australasia 2012, the Automated and reproducible analysis of NGS data (ARANGS12), Beyond the Genome 2012, and ICG Americas 2012.
See the Galaxy Events Google Calendar for details on these and other events.
Several new repositories were added to the Galaxy Tool Shed in September.
htseq_count: Count aligned reads (SAM/BAM) that overlap genomic features (GFF)
DNAClust: tools for Phylogenetic clustering
fastq_groomer_parallel: a multithreaded implementation of FASTQ Groomer
There were two new Galaxy distributions in September:
- A new Galaxy tool that writes other new Galaxy tools? The Tool Factory is in the Galaxy's Main Tool Shed (
toolfactory). Try it now
- Learn how to display multiple versions of a tool in the Galaxy tool panel.
- CloudLaunch Overhaul includes Boto 2.5.2 and simplified instance selection and key generation.
- Release also includes more Tool Shed updates, Framework and API updates, plus Security and Bug fixes.
- NCBI BLAST+ has moved from the Galaxy distribution to the Galaxy's Main Tool Shed.
- Tool Shed is now running Mercurial version 2.2.3. Many updates and refinements including UI/metadata changes - read the full report!
- Streamline local setup with the Reference Genome rsync Server: same builds and indexes as on the public Galaxy Main instance.
- More updates to Output and Error Handling including updated documentation and enhancements to exit code checks.
- TopHat2 / Bowtie2 latest support includes Tophat2 fusions output, Bowtie2 sorted BAMs, and a new RNA-seq Tutorial.
- Trackster updates include improved support for bigWig / bigBed, new support for bedGraph, and a new search feature for GFF / GTF / BED datasets.
- Plus many other Workflow, API, Source, UI features and a summary of recent Galaxy Update highlights.
- Rutger Vos shows how to add a phylotastic service to Galaxy and use phylotastic tools inside Galaxy
- ENCODE Virtual Machine and Cloud Resource is now available.
- Galaxy tutorial from 2012 GMOD Summer School is now available on the http://gmod.org/wiki/|GMOD wiki.
- ISCB Wikipedia Competition launched and the Galaxy Wikipedia page is eligible.