|JBrowse in Galaxy
JBrowse is a fast, embeddable genome browser built completely with
Thus, it makes an ideal fit with Galaxy, especially for use as a
workflow summary. E.g. annotate a genome, then visualise all of the
associated datasets as an interactive HTML page. This tool MUST be whitelisted
(or ``sanitize_all_html=False`` in galaxy.ini) to function correctly.
It is recommended to install this wrapper via the Galaxy Tool Shed.
The Galaxy tool interface writes out a xml file which is then used to generate
the visualizations. An example used during development/testing can be seen in
`test-data/*/test.xml`. The format is in no way rigorously defined and is
likely to change at any time! Beware. ;)
- UPDATED to JBrowse 1.16.11
- UPDATED to JBrowse 1.16.10
- ADDED GALAXY_JBROWSE_SYMLINKS environment variable: if set, the tool will make symlinks to bam/bigwig files instead of copying them
- UPDATED to JBrowse 1.16.9
- UPDATED to JBrowse 1.16.8
- UPDATED to JBrowse 1.16.5
- UPDATED to JBrowse 1.16.4
- ADDED filter too big metadata
- CHANGED default value for topLevelFeatures (gene subfeatures are now inferred) and style.className (feature style was fixed)
- UPDATED to JBrowse 1.16.2
- ADDED support for NeatHTMLFeatures and NeatCanvasFeatures track types
- UPDATED to JBrowse 1.16.1
- ADDED support for MultiBigWig plugin
- ADDED support for tabix indexing of fasta and gff
- ADDED support for REST and SPARQL endpoints
- ADDED option to change chunk size for BAM tracks
- FIXED loading of VCF files. They were gzipped and the URLs were incorrect
- FIXED metadata on tracks types other than GFF+HTML
- FIXED infrastructure URL parsing (and embedding in links) for some tracks
- REMOVED support for selecting multiple genomes as input due to tracking of track metadata
- REMOVED support for themes as JBrowse no longer allow runtime loading of plugins
- 0.7 Support for plugins (currently GC Content, Bookmarks, ComboTrackSelector),
- 0.5.2 Support for CanvasFeatures options.
- 0.5.1 Support for contextual menus. Conda tests.
- 0.5 Update existing instances on disk. Index names. Support HTML tracks
instead of Canvas. Support default tracks. General JBrowse optinos
- 0.4 Support for dataset collections and customisation of tracks including
labelling, colours, styling. Added support for genetic code selection.
Fixed package installation recipe issues.
- 0.3 Added support for BigWig, etc.
- 0.2 Added support for BAM, Blast, VCF.
- 0.1 Initial public release.
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