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Version: 25.2

Upgrade deployment

This page outlines the steps to upgrade your database instance and Platform Enterprise installation to version 25.2, including special considerations for upgrading from versions prior to 25.1.

note
  • Make a backup of your Platform database prior to upgrade.
  • If you are upgrading from a version prior to 25.1, complete all intermediate major version upgrades before upgrading to 25.2.
  • Ensure that no pipelines are in a running state during this upgrade as active run data may be lost.

Considerations for versions prior to 24.1​

  • If you are upgrading from a version older than 23.4.1, update your installation to version 23.4.4 first, before updating to version 25.2 with the steps on this page.

Considersations for versions 24.1 - 25.1​

  • OIDC Secrets injection modifications

    The auth-oidc-secrets Micronaut environment has been replaced with oidc-token-import. If you use this configuration, you must change the MICRONAUT_ENV environment variable in the manifest during the migration process. If you activate the feature with the TOWER_OIDC_TOKEN_IMPORT environment variable, no changes are needed.

  • MariaDB driver: New MySQL connection parameter required

    MariaDB driver 3.x requires the permitMysqlScheme=true parameter in the connection URL to connect to a MySQL database:

    jdbc:mysql://<domain>:<port>/tower?permitMysqlScheme=true

    All deployments using a MySQL database (regardless of version) must be updated when upgrading to Platform version 24.1 or later.

  • Redis version change and property deprecation

    • From Seqera Enterprise version 24.2, Redis version 6.2 or greater is required, and the stable and generally available version 7.4.5 is strongly recommended.
    • From Seqera Enterprise version 24.2, redisson.* configuration properties are deprecated. If you have set redisson.* properties directly previously, do the following: • Replace /redisson/* references in AWS Parameter Store entries with TOWER_REDIS_*. • Replace redisson.* references in tower.yml with TOWER_REDIS_*.
      note

      Set TOWER_REDIS_* values directly in the tower.yml or AWS Parameter Store entry (for example, TOWER_REDIS_URL: redis://...).

  • Micronaut property key changes

    In version 24.1, the property that determines the expiration time of the JWT access token (used for authenticating web sessions and Nextflow-Platform interactions) has changed:

    PreviousNew
    micronaut.security.token.jwt.generator.access-token.expirationmicronaut.security.token.generator.access-token.expiration

    Enterprise deployments that have customized this value previously will need to adopt the new format.

Version 25.2 upgrade considerations​

Secret key rotation requires backup and careful configuration

To configure secret key rotation:

  • To prevent data loss, perform a backup of your Platform database and securely back up your current crypto secret key before enabling and performing key rotation.
  • All backend pods or containers for your Enterprise deployment must contain the same previous and new secret key values in their configuration.
  • All backend pods or containers must be in a ready/running state before starting the Platform cron service.

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.

  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. Restart the application.
  4. 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.
  5. If you're using Amazon RDS or other managed database services:
    1. Stop the application.
    2. Upgrade your database instance.
    3. Restart the application.
  6. 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.