<commit_before>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
=======

- 0.8

    - ADDED
    - 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
<commit_msg>update changelog<commit_after>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
=======

- 0.8 aka 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

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