Development News Brief

Get Galaxy

getgalaxy.org

• new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
• upgrade: % hg pull -u -r 63bc46cc73b7

News & Events

• Make your plans!! GCC2012
• New Galaxy Group @ CiteULike
• Find it now with Custom Galaxy Web Searches
• New low-volume mailing list: [Galaxy-Announce](/news/New Galaxy-Announce Mailing List/)

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)

• Recent publication: Jeremy Goecks, Kanwei Li, Dave Clements, Team, The Galaxy, James Taylor, The Galaxy Track Browser: Transforming the genome browser from visualization tool to analysis tool. Biological Data Visualization (BioVis), 2011 IEEE Symposium on (October 2011), pp. 39-46.
• Simplified user interface that uses icons exclusively for actions.
• Numerous performance improvements.
• SAM datasets (including very deep) can be visualized.
• All rows for feature tracks--BED, GTF, SAM, BAM--can now be displayed.
• Custom composite tracks now available: any amount of wiggle data can be combined into a single track. See Fig.1.

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" 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

• New features:

  • Add the ability to reset all metadata (for every change set) in a tool shed repository (currently restricted to an admin).
  • Enhance User preferences within a Galaxy tool shed to enable users to elect to receive email when content is first uploaded to a new repository. Also add a new grid interface to enable users to easily manage registering with any tool shed respositories to receive email when changes are made to the selected repositories.

• Existing tool shed fixes:

  • Make the use of the 'require_login' config setting functionally correct for the tool shed, and debug it's use in the Galaxy framework as well.
  • Enhance the process for displaying a workflow in a tool shed repository so that workflows in change sets other than the repository tip can be viewed.
  • Do not allow public user names to be changed within the tool shed if the user has created a tool shed repository.
  • Don't allow repository names to be changed if the repository has been cloned at least 1 time.

• More new tool shed features documented in the following new Galaxy wiki sections:

  • Including proprietary data types that subclass from Galaxy data types in the distribution
  • Including proprietary data types that use class modules contained in your repository
  • Including datatype converters and display applications
  • Automatic installation of Galaxy tool shed repository data types into a local Galaxy instance
  • Getting updates for tool shed repositories installed in a local Galaxy instance
  • Migrating tools from the Galaxy distribution to the Galaxy main tool shed
  • Configuring your Galaxy server to automatically install tools eliminated from the Galaxy distribution
  • Use case: automatically install the Emboss tools and datatypes into a local Galaxy instance

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

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