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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse2 commit 5482aa86f906615d9bddcc32cfbc2d45b24e6345
author iuc
date Fri, 24 Oct 2025 07:50:40 +0000
parents 93fdd696c281
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1 # JBrowse2 in Galaxy
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3 JBrowse is a fast, embeddable genome browser built completely with
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4 JavaScript and HTML5
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6 Thus, it makes an ideal fit with Galaxy, especially for use as a
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7 workflow summary. E.g. annotate a genome, then visualise all of the
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8 associated datasets as an interactive HTML page. This tool MUST be added
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9 to the "HTML Rendered" allow list in the Galaxy admin panel to function correctly.
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11 ## Installation
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13 It is recommended to install this wrapper via the Galaxy Tool Shed.
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15 ## Running Locally
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17 The Galaxy tool interface writes out a xml file which is then used to generate
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18 the visualizations. An example used during development/testing can be seen in
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19 `test-data/*/test.xml`. The format is in no way rigorously defined and is
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20 likely to change at any time! Beware. ;)
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22 ## Testing with Planemo
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24 The tool comes with standard tests that can be run with `planemo run`.
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26 If you want to make manual tests with `planemo serve`, it is a bit more complex.
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27 If you do it, you will notice that you cannot see any tool output. That's because JBrowse2 needs to be served
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28 by a HTTP server supporting byte-range requests. Planemo does not by default.
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30 Here comes a hacky solution, that works (but is a bit ugly, sorry).
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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:
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33
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34 ```yaml
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35 services:
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36
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37 proxy:
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38 image: quay.io/abretaud/nginx-ldap:latest # This a basic Nginx image, any other classic Nginx image should work
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39 volumes:
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40 - "./nginx/conf:/etc/nginx/conf.d"
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41 - "/tmp/:/tmp/:ro"
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42 network_mode: "host"
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43 ```
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44
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45 And the mounted `nginx.conf` file:
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46
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47 ```text
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48 server {
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49 listen 80;
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50 server_name ~.;
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51
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52 location /_x_accel_redirect/ {
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53 internal;
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54 alias /;
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55 }
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56
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57 location / {
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58 client_max_body_size 50g;
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59 add_header Accept-Ranges bytes;
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60 proxy_redirect http://localhost:9090/ http://$host;
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61 proxy_pass http://localhost:9090/;
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62 proxy_force_ranges on;
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63 proxy_pass_request_headers on;
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64 }
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65 }
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66 ```
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67
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68 Launch it with `docker compose up -d`.
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69
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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`:
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72 In the `local_galaxy_config` function around line 422, in the `properties.update(...)` call, add this line:
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74 `nginx_x_accel_redirect_base="/_x_accel_redirect",`
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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.
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78 Now you can access your Planemo Galaxy instance at 2 adresses:
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80 - http://localhost:9090/ : the usual Planemo address, file uploads will work, but you can't access JBrowse2 tool output
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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)
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83 ## TODO list
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84
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85 - Support more display options (bug: https://github.com/GMOD/jbrowse-components/issues/5148)
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86 - Reimplement auto coloring of features (custom plugin like https://jbrowse.org/jb2/docs/config_guides/customizing_feature_colors/ ?)
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87 - Support more plugins from https://jbrowse.org/jb2/plugin_store/
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88 - Support Circular view
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
89 - Support SV inspector/spreadsheet views
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
90 - Investigate using CSI indexing instead of TBI for large chromosomes (https://github.com/GMOD/jbrowse-components/issues/4565#issuecomment-2361153737)
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
91 - Synteny: add support for .out (MashMap) .chain (UCSC), .delta (mummer) and .anchors (mcscan) inputs