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Repository jbrowse
Name: jbrowse
Owner: iuc
Synopsis: JBrowse Genome Browser integrated as a Galaxy Tool
JBrowse is a fast, extensible JS+HTML5 genome browser.

This repository contains a couple of tools aimed at building up a complete
JBrowse Genome Browser deployment from raw data files such as gff3, bed, bam,
vcf, blastxml, and more...

The tools produce a ready-to-deploy HTML file and associated processed
datasets, allowing visualization of the genome either from within Galaxy, or
outside of Galaxy.

The tool must be whitelisted for HTML content. If BAM files are displayed, it
must be served from an apache or nginx server implementing sendfile.
Content homepage:
Clone this repository: hg clone
Type: unrestricted
Revision: 43:4542035c1075
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Repository README files - may contain important installation or license information

JBrowse in Galaxy ================= JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5 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. Installation ============ It is recommended to install this wrapper via the Galaxy Tool Shed. Running Locally =============== 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. ;) History ======= - 1.16.11+galaxy0 - UPDATED to JBrowse 1.16.11 - 1.16.10+galaxy0 - 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 - 1.16.9+galaxy0 - UPDATED to JBrowse 1.16.9 - 1.16.8+galaxy0 - UPDATED to JBrowse 1.16.8 - 1.16.5+galaxy0 - UPDATED to JBrowse 1.16.5 - 1.16.4+galaxy0 - 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) - 1.16.2+galaxy0 - UPDATED to JBrowse 1.16.2 - ADDED support for NeatHTMLFeatures and NeatCanvasFeatures track types - 1.16.1+galaxy0 - 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), track metadata - 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. Wrapper License (MIT/BSD Style) =============================== Permission to use, copy, modify, and distribute this software and its documentation with or without modifications and for any purpose and without fee is hereby granted, provided that any copyright notices appear in all copies and that both those copyright notices and this permission notice appear in supporting documentation, and that the names of the contributors or copyright holders not be used in advertising or publicity pertaining to distribution of the software without specific prior permission. THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

Contents of this repository

Name Description Version Minimum Galaxy Version
upgrades the bare data directory to a full JBrowse instance 1.16.11+galaxy0 16.01
genome browser 1.16.11+galaxy0 16.01

Sequence Analysis - Tools for performing Protein and DNA/RNA analysis
Visualization - Tools for visualizing data