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DevNewsBriefs/2012_01_20

January 20, 2012 Galaxy Development News Brief

Get Galaxy

getgalaxy
  • getgalaxy.org

  • new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist

  • upgrade: % hg pull -u -r 63bc46cc73b7

News & Events

Object Store

Galaxy now has a layer between the front end and disk files, and this layer is the Object Store. It allows Galaxy installations to make use of data living in more than simply a single filesystem of locally mounted disk - there are backends for a distributed store (many locally accessible filesystems) or Amazon S3 (in development). Configuration is trivial via the Galaxy config file. See the new object_store option and those following it!

Tools

  • TopHat:

    • Wrapper accepts versions 1.3.1-1.4.0, with at least 1.3.3 recommended. 1.4.0 is preferred.
    • Galaxy Main is now running version 1.4.0.

  • Cufflinks, CuffCompare, CuffDiff:

    • Wrapper accepts versions 1.1.0-1.3.0. 1.3.0 is preferred.
    • Galaxy Main is now running version 1.3.0 for all Cuff* tools.

  • SAMTools mpileup:

    • Wrapper for use in local instances.
    • Not available on Galaxy Main at this time.

  • GenomeSpace import from file browser tool updated to use their newer API.

  • EBI ENA SRA tool contributed by Iain Cleland.

  • Picard Interval List to BED6 converter added.

  • UCSC VCF external display application added.

Galaxy Track Browser (Trackster)

Images/NewsGraphics/2012_01_20_composite-tracks.png
Fig. 1 shows a Visualization of a "rainbow" composite track generated via a "drag-and-drop" method within the Trackster UI itself. The top three individual conservation tracks are combined into a fourth single composite track underneath.

Workflows

  • SAM merge functionality for job splitting.
  • Default static wrapping now works with favicon.ico and robots.txt (and other static files that may need to be mapped to in the future).
  • Provide default for robots.txt being pulled from config.
  • The email workflow action now happens even on job failure.

Source

  • User interface (UI): A history item's details page (linked from the "View Details" Images/Icons/HistoryInfo.png icon) now contains links to the STDOUT and STDERR captured when running a tool's job command line.

  • Job Management: A new setting in the Galaxy config file, cleanup_job can take one of three values, always (the default), never, or onsuccess. This controls when temporary data, such as a job's working directory, external metadata files, and DRM output/error files are cleaned up.

  • JQuery updated to 1.7.1

  • Updated all tools which were manually filtering on tool_data_tables to determine paths to use built-in param.fields.path.
  • Allow select_param.fields.name method of accessing additional attributes from dynamic options work for multiple selects.
  • Merged in hanfeisun/galaxy-central-i18n (pull request #26).
  • Enhance the datatypes registry to:
    • (a) enable use of config files that do not include a "sniffers" tag set section
    • (b) not load a datatype if the registry already includes a datatype with that extension
  • Enhance the datatypes registry so that it can be persisted as an xml file, which is then used for all tools instead of the datatypes config file.
  • Eliminate all references and support for datatype indexers since they have never been used - datatype converters do the same thing.
  • Security: sanitize output anytime a raw text/html dataset is served via dataset/display.
  • Security: sanitizer also now removes javascript content from sanitized anchors, and correctly prevents a whitespace loophole.
  • ObjectStore: Variable multiple outputs (collect_primary_datasets) and components that use collect_child_datasets tuned for new process.

Tool Shed

Tool Shed Contributions

  • New in the Tool Shed:

    • garli, tandem_repeats_finder, by malex

    • data_nfs - Import/export to FTP/NFS directories, by Ed Kirton

    • tapdance - by Jesse Erdmann

    • bedtools - by Aaron Quinlan

    • ncbo_services - by Mikel Egaña Aranguren

    • repeat_masker, trna_prediction, glimmer3, glimmer_hmm - by Björn Grüning

  • Updated:
    • ssr_marker_design - by John McCallum

    • fastq_paired_unpaired, mira-assembler - by Peter Cock

Bug Fixes

bugs
  • Support display of extra files/composite types in published items. Fixes 628

  • Standardize code and error messages on 'public name' rather than 'username'
  • When exporting a history archive, use user dataset names rather than Galaxy dataset names. Fixes 680

  • Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Fixes 610

  • Escape backslashes and quotes in name attributes for UCSC external display applications which use bigDataUrls. Remove no longer required strip_https attribute. Fixes 627

  • UCSC BAM display will now pass the pairEndsByName attribute. Fixes 455

  • Allow tools with zero inputs. Fixes 463

  • Allow not specifying a value attribute for an optional tool parameter. Partially fixes 661

  • Add non_zero method to ToolParameterValueWrappers. Allows boolean checks directly on wrapped parameter values. Fixes 661

  • Display application configuration not supported in Automatic Installation. Fixes 695

  • Data types configuration not supported in Automatic Installation. Fixes 696

  • Fix for browsing libraries in IE. Previously json2 wasn't being loaded, which is needed in IE for jstorage to work.


About Galaxy

GalaxyProject.org

The GalaxyTeam is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.

Galaxy is supported in part by NSF, NHGRI, the Huck Institutes of the Life Sciences, and The Institute for CyberScience at Penn State, and Emory University.

Join us at Twitter @galaxyproject