Development News Brief
% hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
% hg pull -u -r 63bc46cc73b7
- Make your plans!! GCC2012
- New Galaxy Group @ CiteULike
- Find it now with Custom Galaxy Web Searches
- New low-volume mailing list: Galaxy-Announce
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.
- 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.
- 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
STDERRcaptured when running a tool's job command line.
- Job Management: A new setting in the Galaxy config file,
cleanup_jobcan take one of three values,
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:
- 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
- New in the Tool Shed:
garli, tandem_repeats_finder, by
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 https://bitbucket.org/galaxy/galaxy-central/issue/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 https://bitbucket.org/galaxy/galaxy-central/issue/680
- Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Fixes https://bitbucket.org/galaxy/galaxy-central/issue/610
- Escape backslashes and quotes in name attributes for UCSC external display applications which use bigDataUrls. Remove no longer required strip_https attribute. Fixes https://bitbucket.org/galaxy/galaxy-central/issue/627
- UCSC BAM display will now pass the pairEndsByName attribute. Fixes https://bitbucket.org/galaxy/galaxy-central/issue/455
- Allow tools with zero inputs. Fixes https://bitbucket.org/galaxy/galaxy-central/issue/463
- Allow not specifying a value attribute for an optional tool parameter. Partially fixes https://bitbucket.org/galaxy/galaxy-central/issue/661
- Add non_zero method to ToolParameterValueWrappers. Allows boolean checks directly on wrapped parameter values. Fixes https://bitbucket.org/galaxy/galaxy-central/issue/661
- Display application configuration not supported in Automatic Installation. Fixes https://bitbucket.org/galaxy/galaxy-central/issue/695
- Data types configuration not supported in Automatic Installation. Fixes https://bitbucket.org/galaxy/galaxy-central/issue/696
- Fix for browsing libraries in IE. Previously json2 wasn't being loaded, which is needed in IE for jstorage to work.