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January 2013 Galaxy Update

Galaxy Updates

Welcome to the January 2013 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:

  • "Latent Regulatory Potential of Human-Specific Repetitive Elements," by Michelle C. Ward, Michael D. Wilson, Nuno L. Barbosa-Morais, et al.; Molecular Cell (December 2012) → Analysis workflows are at [https://usegalaxy.org/workflow/list_published|Galaxy Main](https://usegalaxy.org/workflow/list_published|Galaxy Main).
  • There are now 599 papers in the Galaxy CiteULike Group.

    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.


    2013 Galaxy Community Conference (GCC2013)

    Training Day Topic Nominations

    2013 Galaxy Community Conference (GCC2013) Training Day

    Nominations are now open for Training Day topics for the 2013 Galaxy Community Conference (GCC2013). GCC2013 will start on 30 June with a Training Day featuring 4 parallel tracks, each with three, two hour workshops, for a total of twelve sessions.

    Any topic of interest to the Galaxy Community can be nominated. See what's been nominated so far (and what was offered at GCC2012). Topics can be repeats from last year or brand new, and you are encouraged to nominate as many topics as you like.

    Topic nomination closes 11 January.


    Molecular Life Science at the University of Oslo    The Research Council of Norway    Functional Genomics    Elixer

    Please join us in thanking Molecular Life Science at the University of Oslo, The Research Council of Norway, Functional Genomics and Elixer for hosting and funding the 2013 Galaxy Community Conference.

    Amazon Web Services

    We are also pleased to announce 'Amazon Web Services as the GCC2013 Training Day Sponsor. There are still several sponsorships still available. Please contact the Organizers if your organization would like to help sponsor this event.

    January GalaxyAdmins Web Meetup

    January Galaxy Admins Web Meetup

    The next GalaxyAdmins Meetup will be Wednesday, January 16, 2013 at 10am US central time. John Chilton of the Minnesota Supercomputing Institute will cover "Deploying Production Galaxy Environments on OpenStack with CloudBioLinux and CloudMan."

    Please join us.

    Other 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
    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
    March 26-28 RNA Technologies and Analysis Workshop DOE JGI User Meeting Zhong Wang, Len Pennacchio
    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 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan
    June 30 - July 2 2013 Galaxy Community Conference (GCC2013) University of Oslo, Oslo, Norway Galaxy Outreach


    New Galaxy Distributions

    Dec 20, 2012 Distribution

    **Highlights:** * **Required Metadata Reset** for instances running **[Tool Shed](http://wiki.galaxyproject.org/ToolShed)** repositories. Be sure to **[learn how](http://wiki.galaxyproject.org/ResettingMetadataForInstalledRepositories)**. * **Simplified tool config**: all tools (including tool shed repos) can now have handlers and runners assigned based on their "short id". * **New** [GFF](http://wiki.galaxyproject.org/Learn/Datatypes#GFF)/[GFF3](http://wiki.galaxyproject.org/Learn/Datatypes#GFF3) annotation support for **[Cuffcompare/merge/diff](http://cufflinks.cbcb.umd.edu/manual.html)**. * **More Updated** tools: **[TopHat2](http://tophat.cbcb.umd.edu/manual.html)**, **[Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml)**. * **Multiple pull-requests** contributed by community (thanks!): **[#83](https://bitbucket.org/galaxy/galaxy-central/pull-request/83/allow-a-datatypes-merge-method-to)**, **[#85](https://bitbucket.org/galaxy/galaxy-central/pull-request/85/another-round-of-bug-fixes-and)**, **[#90](https://bitbucket.org/galaxy/galaxy-central/pull-request/90/patch-to-make-extended_metadata-loader)**, **[#91](https://bitbucket.org/galaxy/galaxy-central/pull-request/91/fixing-missing-jobwrapper-import)**. * **Issue tracking help** is now covered in detailed in our new wiki: **[Using the Galaxy Issue Board](http://wiki.galaxyproject.org/Issues)** * **[GCC2013 Training Day Topic Nominations](http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay) are now open** through ***[January 11th](http://wiki.galaxyproject.org/Events/GCC2013/KeyDates)*** * Plus more **[Tool Shed](http://wiki.galaxyproject.org/ToolShed)** updates, **Bug Fixes**, and improvements to **Trackster, UI, Libraries, and Histories**.
    new:     $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
    upgrade: $ hg pull -u -r 36ad8aa7b922

    Dec 3, 2012 Distribution

    **Highlights:** * **NGS: Mapping** tools **[Bowtie](http://bowtie-bio.sourceforge.net/index.shtml)** and **[Lastz](http://www.bx.psu.edu/~rsharris/lastz/)** have moved from the **[Galaxy distribution](https://bitbucket.org/galaxy/galaxy-dist)** to the **[Galaxy Main Tool Shed](http://toolshed.g2.bx.psu.edu/)**. * Improvements in the display of **[http://wiki.galaxyproject.org/ToolShed](http://wiki.galaxyproject.org/ToolShed)** repository dependencies and contents. * More **[Tool Shed](http://toolshed.g2.bx.psu.edu/)** updates including details of the [Functional test framework](http://wiki.galaxyproject.org/HostingALocalToolShed#Functional_test_framework_for_the_tool_shed), a new hgweb.config file and `HgWebConfigManager` tool, plus other management features. * Updated **UI** display and functionality for datasets and histories: new **paused** state and "resume/paused" toggle, new **History menu options** (seen at right →), and improved **Scatterplot** visualizations. * The **SGE** job runner has now been fully deprecated and replaced with **DRMAA**. * Several enhancements to aid with **reproducibility**: "Re-run" and "Extract workflow" validates datasets and tools, respectively, and a new data tables registry within the Administration menu, along with associated tools, corrects or warns about tool migration issues. * Highlights from the new Galaxy **[CloudMan](http://usegalaxy.org/cloud)** release.
    new:     $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
    upgrade: $ hg pull -u -r f364d992270c

    Tool Shed Contributions

    Galaxy Tool Shed

    It was a banner month for Galaxy Tool Shed contributions:

    • snp_annotation: Split vcf file, variant effect predictor, protseq, netphos, mitoprot, conservation, gpi & join results.
    • Two Bismark repositories were created:

      • methylation_analysis_bismark:

        • Bismark: bisulfite mapper, methylation caller;
        • Methylation Extractor: methylation information for individual cytosines;
        • Methylation by region: create a bedgrapgh with methylation percentages aggregated by region;
        • Differential Methylation: comparison of two samples' methylation by region
      • bismark:

        • Methylation extractor
        • Bisulfite mapper (bowtie)
        • Bisulfite mapper (bottie2)
    • bedtools_annotate: Annotate the depth X breadth of coverage of features from multiple files
    • add_value, change_case, condense_characters, convert_characters, cut_columns, merge_cols, remove_beginning, show_beginning, show_tail, trimmer, : All moved from distribution to tool shed.
    • assessing_target_enrichment: Workflows to compute coverage on targeted regions when using hybrid-capture
    • matrix_normalization: Normalization tool for matrix formatted data
    • plot_distribution: plot distribution of numeric data in table format (either single data column or entire matrix)
    • bamedit: Merging, splitting, filtering, and QC of BAM files
    • macs2: Model-based Analysis of ChIP-Seq
    • peakranger: multi-purpose, ultrafast ChIP Seq peak caller
    • spp_phantompeak: SPP cross-correlation analysis package
    • These protein tools were contributed by the Galaxy-P project:

      • pride_biomart: Fetch data from PRIDE's BioMart server.
      • dbbuilder: Download protein databases from common sources.
      • msconvert: Tool wrappers for the msconvert application distributed as part of Proteowizard.
      • ProteinPilot: Tools for working with ProteinPilot.
      • decoyfasta: Transproteomic pipeline decoyFASTA tool.
      • ms2preproc: Tool wrapper for ms2preproc.
      • digestdb: Tool wrapper for transproteomic pipeline application digestdb.
      • openms: Tool wrappers for various applications that contained in the OpenMS suite.
      • mzxml2search: Use MzXML2Search to convert peak lists.
    • seq2hla: HLA typing from RNA-Seq sequence reads
    • snp_annotation: Split vcf file, variant effect predictor, protseq, netphos, mitoprot, conservation, gpi and join result files.
    • trim_galaore: Wrapper script that makes use of the publicly available adapter trimming tool Cutadapt and FastQC for optional quality control once the trimming process has completed.

    Other News