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install-methylationplugin.md

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Installing bhofmei/jbplugin-methylation on apollo-037

Context

Client mtan_user on apollo-037 needed the MethylationPlugin (bhofmei/jbplugin-methylation) in Apollo's embedded JBrowse1 for methylation-track visualisation. The same plugin runs on apollo-021 (installed manually years ago by a previous sysadmin). This doc records the sequence that actually got it working on 037 on 2026-07-07, including the false starts, so future occurrences can skip them.

Result: plugin baked into the WAR shipped from apollo-deploy, extracted onto apollo-037 by Tomcat, verified visible in the analytics ping's plugins= list, and rendering methylation tracks (WT HTML Methylation, etc.) on the "Test OK (Methylation)" organism.

Installatioan approach

  1. Confirmed a pre-baked variant tarball already existed on the deployment server: /opt/apollo_files/Apollo-2.8.1+methylation-Ubuntu-deploy-20250606.tar.gz (~238MB, plugin verified inside Apollo-2.8.1/target/apollo-2.8.1.war → jbrowse/dist/main.bundle.js grep MethylationPlugin > 0).
  2. Pointed the deploy symlink at it: 
    ssh apollo-deploy 'sudo ln -sfn ../Apollo-2.8.1+methylation-Ubuntu-deploy-20250606.tar.gz \
                                 /opt/apollo_files/deploy/Apollo-2.8.1.tar.gz'
  3. Shipped the tarball to apollo-037 manually and extracted it (a --tags deploy playbook run cannot do this — see the ansible/playbooks/README.md tarball-variant section for the reasoning): 
    ssh apollo-deploy 'scp /opt/apollo_files/Apollo-2.8.1+methylation-Ubuntu-deploy-20250606.tar.gz \
                       ubuntu@apollo-037.genome.edu.au:/tmp/Apollo-2.8.1.tar.gz'
ssh ubuntu@apollo-037.genome.edu.au 'sudo mv /tmp/Apollo-2.8.1.tar.gz /opt/Apollo-2.8.1.tar.gz
                                     sudo rm -rf /opt/Apollo-2.8.1
                                     cd /opt && sudo tar -xzf Apollo-2.8.1.tar.gz
                                     sudo chown -R root:root /opt/Apollo-2.8.1'
  4. Ran the ansible deploy chain: 
    ansible-playbook playbook-build-nectar-apollo.yml \
  --inventory-file hosts --limit apollo-037.genome.edu.au \
  --tags deploy \
  --extra-vars "apollo_instance_number=37 apollo_subdomain_name=mtan"
  5. Verified: 
    ssh ubuntu@apollo-037.genome.edu.au \
  'sudo grep -c MethylationPlugin /var/lib/tomcat9/webapps/apollo/jbrowse/dist/main.bundle.js'
# > 0 = plugin baked into the extracted webapp
  6. In the browser, hard-refresh, use the organism switcher, click a methylation track. The jbrowse analytics ping (jbrowse.org/analytics/clientReport?...) should list MethylationPlugin in its plugins= query param.

Rollback

Symlink swap back to the stock tarball, then rerun steps 3 + 4:

ssh apollo-deploy 'sudo ln -sfn ../Apollo-2.8.1-Ubuntu-deploy-20250528.tar.gz \
                                 /opt/apollo_files/deploy/Apollo-2.8.1.tar.gz'

Per-organism activation

Once the plugin is baked into the WAR (steps above), no top-level plugins block is required in any organism's trackList.json — the plugin's Dojo AMD package is already registered globally via the compiled bundles. Activation is done per track, by pointing the relevant track's storeClass and type at the plugin's classes. For a bigwig methylation track:

{
  "storeClass" : "MethylationPlugin/Store/SeqFeature/MethylBigWig",
  "type"       : "MethylationPlugin/View/Track/Wiggle/MethylPlot",
  ...
}

Files live on the NFS server: /mnt/user-data/nectar/apollo-037/apollo_data/<Organism>/trackList.json. No Tomcat restart needed after editing; hard-refresh the browser to bypass client-side caching.