new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r 63bc46cc73b7
News & Events
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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!
- 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.
- 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.
- 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.
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.
- 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.
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.
ObjectStore: Variable multiple outputs (collect_primary_datasets) and components that use collect_child_datasets tuned for new process.
- 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:
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
ssr_marker_design - by John McCallum
fastq_paired_unpaired, mira-assembler - by Peter Cock
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.
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