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+# JBrowse2 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 added
+to the "HTML Rendered" allow list in the Galaxy admin panel 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. ;)
+
+## Testing with Planemo
+
+The tool comes with standard tests that can be run with `planemo run`.
+
+If you want to make manual tests with `planemo serve`, it is a bit more complex.
+If you do it, you will notice that you cannot see any tool output. That's because JBrowse2 needs to be served
+by a HTTP server supporting byte-range requests. Planemo does not by default.
+
+Here comes a hacky solution, that works (but is a bit ugly, sorry).
+
+First you need to start a Nginx server that will act as a proxy to the local Galaxy server launched by `planemo serve`. This can be done easily with a docker-compose.yml file like this:
+
+```yaml
+services:
+
+  proxy:
+    image: quay.io/abretaud/nginx-ldap:latest  # This a basic Nginx image, any other classic Nginx image should work
+    volumes:
+        - "./nginx/conf:/etc/nginx/conf.d"
+        - "/tmp/:/tmp/:ro"
+    network_mode: "host"
+```
+
+And the mounted `nginx.conf` file:
+
+```text
+server {
+    listen 80;
+    server_name  ~.;
+
+    location /_x_accel_redirect/ {
+        internal;
+        alias /;
+    }
+
+    location / {
+        client_max_body_size 50g;
+        add_header Accept-Ranges bytes;
+        proxy_redirect   http://localhost:9090/       http://$host;
+        proxy_pass http://localhost:9090/;
+        proxy_force_ranges on;
+        proxy_pass_request_headers      on;
+    }
+}
+```
+
+Launch it with `docker compose up -d`.
+
+Then you need to make a small modification of Planemo's code (do it in a dedicated virtualenv), supposing you have installed it in `~/venvs/planemo`, edit `~/venvs/planemo/lib/python*/site-packages/planemo/galaxy/config.py`:
+
+In the `local_galaxy_config` function around line 422, in the `properties.update(...)` call, add this line:
+
+`nginx_x_accel_redirect_base="/_x_accel_redirect",`
+
+Now run `planemo serve`, and then run a `chmod a+rx /tmp/tmpxxxx`, where `/tmp/tmpxxxx` is the directory where Planemo is running Galaxy from.
+
+Now you can access your Planemo Galaxy instance at 2 adresses:
+
+- http://localhost:9090/ : the usual Planemo address, file uploads will work, but you can't access JBrowse2 tool output
+- http://localhost:80/ : the same Galaxy server where you *can* access JBrowse2 tool output (don't forget to add the tool in the "HTML Rendered" allow list in the admin panel)
+
+## TODO list
+
+- Support more display options (bug: https://github.com/GMOD/jbrowse-components/issues/5148)
+- Reimplement auto coloring of features (custom plugin like https://jbrowse.org/jb2/docs/config_guides/customizing_feature_colors/ ?)
+- Support more plugins from https://jbrowse.org/jb2/plugin_store/
+- Support Circular view
+- Support SV inspector/spreadsheet views
+- Investigate using CSI indexing instead of TBI for large chromosomes (https://github.com/GMOD/jbrowse-components/issues/4565#issuecomment-2361153737)
+- Synteny: add support for .out (MashMap) .chain (UCSC), .delta (mummer) and .anchors (mcscan) inputs