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Version: 24.2

Upgrade deployment

Follow these steps to upgrade your database instance and Platform Enterprise installation:

note

From Seqera Enterprise version 23.4, MySQL 8 is the only supported database version. If you are upgrading from a version prior to 23.4 and running MySQL 5.6 or 5.7, you must upgrade your database to MySQL 8 before upgrading to version 24.2. See General upgrade steps for database upgrade instructions.

General upgrade steps​

caution

The database volume is persistent on the local machine by default if you use the volumes key in the db or redis section of your docker-compose.yml file to specify a local path to the DB or Redis instance. If your database is not persistent, you must back up your database before performing any application or database upgrades.

info

Starting from version 26.1, the frontend image running as root user will be deprecated. We recommend starting to switch to the root-less image (also known as "unprivileged" image) during this upgrade.

  1. Make a backup of the Seqera database. If you use the pipeline optimization service and your groundswell database resides in a database instance separate from your Seqera database, make a backup of your groundswell database as well.

  2. Download the latest versions of your deployment templates and update your Seqera container versions:

  3. If you're using Studios, download and apply the latest versions of the Kubernetes manifests:

    warning

    If you have customized the default Studios container template images, you must ensure that you update to latest recommended versions. Templates using earlier versions of Connect (than defined in the latest proxy.yml and server.yml) may no longer be supported in your existing Studios environments. Refer to the Studios migration documentation for guidance on migrating to the most recent versions of Connect server and clients.

  4. Restart the application.

  5. If you're using a containerized database as part of your implementation:

    1. Stop the application.
    2. Upgrade the MySQL image.
    3. Restart the application.

  6. If you're using Amazon RDS or other managed database services:

    1. Stop the application.
    2. Upgrade your database instance.
    3. Restart the application.

  7. If you're using the pipeline optimization service (groundswell database) in a database separate from your Seqera database, update the MySQL image for your groundswell database instance while the application is down (during step 4 or 5 above). If you're using the same database instance for both, the groundswell update will happen automatically during the Seqera database update.

Custom deployments​

  • Run the /migrate-db.sh script provided in the migrate-db container. This will migrate the database schema.
  • Deploy Seqera following your usual procedures.

Nextflow launcher image​

If you must host your nf-launcher container image on a private image registry, copy the nf-launcher image to your private registry. Then update your tower.env with the launch container environment variable:

TOWER_LAUNCH_CONTAINER=<FULL_PATH_TO_YOUR_PRIVATE_IMAGE>

caution

If you're using AWS Batch, you will need to configure a custom job definition and populate the TOWER_LAUNCH_CONTAINER with the job definition name instead.

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