Upgrade Varfish Installation

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

Problem with Data Release 20210728 and GRCh37

The data release has a problem with the GRCh37 extra annotations. If you can then use the updated site data 20210728b release. If you already have an instance with 20210728 background data then you can use the following data file.

Download and extract the file and mount it as /data inside the varfish-web container. You can then apply the patch to your database with the following command.

$ docker exec -it varfish-docker-compose_varfish-web_1 python /usr/src/app/manage.py \
    import_tables --tables-path /data --truncate --force

You can find out more details, give feedback, and ask for help in this Github discussion.

v0.23.0 to v1.2.1

This includes all version in between, v0.23.1, …, v1.2.1.

Summary

This are minor bug fix releases and small added features. You should be able to upgrade by just updating your varfish-docker-compose repository clone and calling docker-compose up -d.

v0.23.1 to v0.23.2

Summary

This is a minor bug fix release that improved the deployment of the VarFish Demo and Kiosk sites. You should be able to upgrade by just updating your varfish-docker-compose repository clone and calling docker-compose up -d.

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 Install Scoring with CADD.

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 Miscellaneous Configuration. The default value is also stored in the public repository and thus not very secure.