From ea2174b18615d8a58f00ef598c712220459d32a2 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Tue, 17 Oct 2023 12:35:48 +0200
Subject: [PATCH] add FAQ about upgrading through 22.05

---
 topics/admin/faqs/galaxy-update-22.05.md | 93 ++++++++++++++++++++++++
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 create mode 100644 topics/admin/faqs/galaxy-update-22.05.md

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+---
+title: Updating from 22.01 to 23.0 with Ansible
+area: ansible
+box_type: tip
+layout: faq
+contributors: [hexylena]
+---
+
+Galaxy introduced a number of changes in 22.05 and 23.0 that are extremely important to be aware of during the upgrade process. Namely a new database migration system, and a new required running environment (gunicorn instead of uwsgi).
+
+Unfortunately the scripts to migrate to the new database migration system were only present in 22.05, and then were subsequently removed, so it is **mandatory** to upgrade to 22.05 if you want to go further.
+
+Here is the recommended update procedure with ansible:
+
+1. Update to 22.01 normally
+2. Change the release to 22.05, and run the upgrade
+   1. Galaxy will probably not start correctly here, ignore it.
+   2. Run the database migration manually
+
+      ```
+      GALAXY_CONFIG_FILE=/srv/galaxy/config/galaxy.yml sh manage_db.sh -c /srv/galaxy/config/galaxy.yml upgrade
+      ```
+3. Set the release to `23.0` and make other required changes. There are a lot of useful changes, but the easiest procedure is probably something like:
+
+   1. git clone https://github.com/hexylena/git-gat/
+   2. git checkout step-4
+   3. `vimdiff group_vars/galaxyservers.yml git-gat/group_vars/galaxyservers.yml` (repeat for group_vars/all.yml, group_vars/dbservers.yml, galaxy.yml, requirements.yml, hosts, etc.)
+
+   But the main change is the swap from uwsgi to gravity+gunicorn
+
+   ```diff
+   -  uwsgi:
+   -    socket: 127.0.0.1:8080
+   -    buffer-size: 16384
+   -    processes: 1
+   -    threads: 4
+   -    offload-threads: 2
+   -    static-map:
+   -      - /static={{ galaxy_server_dir }}/static
+   -      - /favicon.ico={{ galaxy_server_dir }}/static/favicon.ico
+   -    static-safe: client/galaxy/images
+   -    master: true
+   -    virtualenv: "{{ galaxy_venv_dir }}"
+   -    pythonpath: "{{ galaxy_server_dir }}/lib"
+   -    module: galaxy.webapps.galaxy.buildapp:uwsgi_app()
+   -    thunder-lock: true
+   -    die-on-term: true
+   -    hook-master-start:
+   -      - unix_signal:2 gracefully_kill_them_all
+   -      - unix_signal:15 gracefully_kill_them_all
+   -    py-call-osafterfork: true
+   -    enable-threads: true
+   -    mule:
+   -      - lib/galaxy/main.py
+   -      - lib/galaxy/main.py
+   -    farm: job-handlers:1,2
+   +  gravity:
+   +    process_manager: systemd
+   +    galaxy_root: "{{ galaxy_root }}/server"
+   +    galaxy_user: "{{ galaxy_user_name }}"
+   +    virtualenv: "{{ galaxy_venv_dir }}"
+   +    gunicorn:
+   +      # listening options
+   +      bind: "unix:{{ galaxy_mutable_config_dir }}/gunicorn.sock"
+   +      # performance options
+   +      workers: 2
+   +      # Other options that will be passed to gunicorn
+   +      # This permits setting of 'secure' headers like REMOTE_USER (and friends)
+   +      # https://docs.gunicorn.org/en/stable/settings.html#forwarded-allow-ips
+   +      extra_args: '--forwarded-allow-ips="*"'
+   +      # This lets Gunicorn start Galaxy completely before forking which is faster.
+   +      # https://docs.gunicorn.org/en/stable/settings.html#preload-app
+   +      preload: true
+   +    celery:
+   +      concurrency: 2
+   +      loglevel: DEBUG
+   +    handlers:
+   +      handler:
+   +        processes: 2
+   +        pools:
+   +          - job-handlers
+   +          - workflow-schedulers
+   ```
+
+   Some other important changes include:
+   - uchida.miniconda is replaced with galaxyproject.conda
+   - usegalaxy_eu.systemd is no longer needed
+   - `galaxy_user_name` is defined in all.yml in the latest git-gat
+   - git-gat also separates out the DB serving into a `dbservers.yml` host group
+
+4. Backup your `venv`, `mv /srv/galaxy/venv/ /srv/galaxy/venv-old/`, as your NodeJS is probably out of date and Galaxy doesn't handle that gracefully
+5. Do any local customs for luck (knocking on wood, etc.)
+6. Run the playbook