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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
author iuc
date Thu, 02 Oct 2025 10:19:44 +0000
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1 # JBrowse2 in Galaxy
2
3 JBrowse is a fast, embeddable genome browser built completely with
4 JavaScript and HTML5
5
6 Thus, it makes an ideal fit with Galaxy, especially for use as a
7 workflow summary. E.g. annotate a genome, then visualise all of the
8 associated datasets as an interactive HTML page. This tool MUST be added
9 to the "HTML Rendered" allow list in the Galaxy admin panel to function correctly.
10
11 ## Installation
12
13 It is recommended to install this wrapper via the Galaxy Tool Shed.
14
15 ## Running Locally
16
17 The Galaxy tool interface writes out a xml file which is then used to generate
18 the visualizations. An example used during development/testing can be seen in
19 `test-data/*/test.xml`. The format is in no way rigorously defined and is
20 likely to change at any time! Beware. ;)
21
22 ## Testing with Planemo
23
24 The tool comes with standard tests that can be run with `planemo run`.
25
26 If you want to make manual tests with `planemo serve`, it is a bit more complex.
27 If you do it, you will notice that you cannot see any tool output. That's because JBrowse2 needs to be served
28 by a HTTP server supporting byte-range requests. Planemo does not by default.
29
30 Here comes a hacky solution, that works (but is a bit ugly, sorry).
31
32 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:
33
34 ```yaml
35 services:
36
37 proxy:
38 image: quay.io/abretaud/nginx-ldap:latest # This a basic Nginx image, any other classic Nginx image should work
39 volumes:
40 - "./nginx/conf:/etc/nginx/conf.d"
41 - "/tmp/:/tmp/:ro"
42 network_mode: "host"
43 ```
44
45 And the mounted `nginx.conf` file:
46
47 ```text
48 server {
49 listen 80;
50 server_name ~.;
51
52 location /_x_accel_redirect/ {
53 internal;
54 alias /;
55 }
56
57 location / {
58 client_max_body_size 50g;
59 add_header Accept-Ranges bytes;
60 proxy_redirect http://localhost:9090/ http://$host;
61 proxy_pass http://localhost:9090/;
62 proxy_force_ranges on;
63 proxy_pass_request_headers on;
64 }
65 }
66 ```
67
68 Launch it with `docker compose up -d`.
69
70 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`:
71
72 In the `local_galaxy_config` function around line 422, in the `properties.update(...)` call, add this line:
73
74 `nginx_x_accel_redirect_base="/_x_accel_redirect",`
75
76 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.
77
78 Now you can access your Planemo Galaxy instance at 2 adresses:
79
80 - http://localhost:9090/ : the usual Planemo address, file uploads will work, but you can't access JBrowse2 tool output
81 - 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)
82
83 ## TODO list
84
85 - Support more display options (bug: https://github.com/GMOD/jbrowse-components/issues/5148)
86 - Reimplement auto coloring of features (custom plugin like https://jbrowse.org/jb2/docs/config_guides/customizing_feature_colors/ ?)
87 - Support more plugins from https://jbrowse.org/jb2/plugin_store/
88 - Support Circular view
89 - Support SV inspector/spreadsheet views
90 - Investigate using CSI indexing instead of TBI for large chromosomes (https://github.com/GMOD/jbrowse-components/issues/4565#issuecomment-2361153737)
91 - Synteny: add support for .out (MashMap) .chain (UCSC), .delta (mummer) and .anchors (mcscan) inputs