Skip to content

Latest commit

 

History

History
41 lines (29 loc) · 1.88 KB

admin_upgrade.rst

File metadata and controls

41 lines (29 loc) · 1.88 KB
Raw

Upgrade Varfish Installation

This section contains upgrade instructions for upgrading your VarFish Server installation using VarFish Docker Compose.

v0.22.1 to v0.23.0

Summary

  • The Docker Compose installer now provides support for setting up CADD score annotation via cadd-rest-api.
  • The environment variable FIELD_ENCRYPTION_KEY should be setup properly by the user.
  • Two new celery queues are needed: maintenance and export.
  • To enable the new and optional feature for uploading variants to SPANR you have to set the environment variable VARFISH_ENABLE_SPANR_SUBMISSION to 1.

Detailed Instructions

Docker Compose: cadd-rest-api

Update your varfish-docker-compose installation with the changes from the Github repository without installing cadd-rest-api. This will give you commented out lines for running one cadd-rest-api-server and multiple cadd-rest-api-celeryd-worker-? containers. For enabling them, follow the instructions in admin_extras_cadd_scripts.

Additional Celery Queues

After updating your varfish-docker-compose.yml file, ensure that you the two additional containers varfish-celeryd-maintenance and varfish-celeryd-export. These will run the background jobs for running maintenance tasks and export results. They will be started when running docker-compose up.

Environment Variable: FIELD_ENCRYPTION_KEY

Set the environment variable in the .env file as documented in admin_config_misc. The default value is also stored in the public repository and thus not very secure.