--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jbrowse2/readme.rst	Wed Jan 03 01:36:39 2024 +0000
@@ -0,0 +1,117 @@
+JBrowse2 in Galaxy
+=================
+
+    JBrowse2 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.
+gunicorn does not support byte range requests, so this tool must be served by nginx
+or other web server, correctly configured to support range requests.
+
+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
+=======
+
+- 2.10.0+galaxy2
+
+    - UPDATED to JBrowse 2.10.0
+    - REMOVED most colour and track control from XML and script.
+    - seems to work well with defaults.
+    - need to document and implement track settings by running the browser locally.
+    - works well enough to be useful in workflows such as TreeValGal.
+    - JB2 seems to set defaults wisely.
+    - not yet ideal for users who need fine grained track control.
+
+- 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.