diff readme.rst @ 7:b04fd993b31e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717

--- a/readme.rst	Tue Jan 09 06:55:34 2024 +0000
+++ b/readme.rst	Wed Jan 17 07:50:52 2024 +0000
@@ -8,92 +8,40 @@
 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.
+The built-in Galaxy gunicorn server does not support byte range requests, so this tool must be proxied by nginx
+or another web server, correctly configured to support range requests. A tiny web server is bundled
+with each JBrowse2 archive - see below.
 
 Installation
 ============
 
-It is recommended to install this wrapper via the Galaxy Tool Shed.
+This wrapper is normally installed by a server administrator from the Galaxy Tool Shed IUC JBrowse2 repository.
 
-Running Locally
-===============
+Local display
+=============
 
-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. ;)
+Each JBrowse2 history item can be downloaded ("floppy disk" icon) to your local disk. There, it can be unzipped into a new directory.
+That directory includes a python script, *jb2_webserver.py* that will run a local web server able to serve byte range requests,
+giving the same view as seen when viewed from the Galaxy history.
+
+From the newly unzipped directory where that file can be found, and with Python3 installed and working,
+
+`python3 jb2_webserver.py`
+
+will open the preconfigured browser using the default web browser application.
 
 History
 =======
 
 - 2.10.0+galaxy2
 
-    - UPDATED to JBrowse 2.10.0
-    - REMOVED most colour and track control from XML and script.
+    - UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0
     - 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)
 ===============================