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Version: 24.2

Upgrade deployment

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

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. JVM memory configuration defaults (recommended): The following JAVA_OPTS environment variable is included in the deployment templates downloaded in the preceding step, to optimize JVM memory settings:

    JAVA_OPTS: -Xms1000M -Xmx2000M -XX:MaxDirectMemorySize=800m -Dio.netty.maxDirectMemory=0 -Djdk.nio.maxCachedBufferSize=262144

    These baseline values are suitable for most deployments running moderate concurrent workflow loads.

    tip

    These are starting recommendations that may require tuning based on your deployment's workload. See Backend memory requirements for detailed guidance on when and how to adjust these values for your environment.

  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.