Extended features¶
Note
The vast majority of the configuration of Pretzel is done via the docker compose yaml and environment files. As such a lot of the below points reference these files located in our github repo.
Modifying the Pretzel API¶
Deploying older Pretzel API versions¶
A complete list of released pretzel images can be found on our dockerhub page.
To change versions just edit the image: field in the docker-compose.yaml file.
api: # node environment
...
image: plantinformaticscollaboration/latest # replace latest with the desired version
docker compose --file docker-compose.prod.yaml --env-file pretzel.compose.prod.env up -d
Deploying custom Pretzel API images¶
If deploying a custom image you will need to build the image from source. See Building custom Pretzel API images
To use the custom image you will need to update the image: field in the docker-compose.yaml file.
api: # node environment
...
image: # Path to the custom image or image tag name
Followed by deploying the new image with the following command:
docker compose --file docker-compose.prod.yaml --env-file pretzel.compose.prod.env up -d
Building custom Pretzel API images¶
In the home directory of the cloned repo run the following commands to build the image:
mkdir -p ~/log/build/docker # create the log directory if it doesn't exist
sudo docker build . > ~/log/build/docker/$logDate
The image tag name will be displayed in the log file. Use this tag name in the image: field in the docker-compose.yaml file. As described in Deploying custom Pretzel API images.
Add a custom landingPage¶
If a directory is provided, this content is displayed in the Pretzel home page before the user logs in. This only supports static html content.
landingPage= # directory containing static html content.
Enabling/Disabling email verification¶
Only enable email verification if you have set up an Amazon SES SMTP email address. Otherwise accounts will be created with no means to verify them.
EMAIL_VERIFY= # ADMIN or NONE
Setting up email verification¶
See Setting an Amazon SES SMTP email address for more information and for the values to use for the following variables.
# EMAIL_ADMIN=user-email-admin@example.com
# EMAIL_HOST=email-smtp.<region>.amazonaws.com
EMAIL_PORT=25
# EMAIL_PASS=...
# EMAIL_USER=...
# EMAIL_FROM=admin@example.com
Enable results caching¶
Added in v3.1.0.
The Pretzel API server will cache results for common requests, enabling them to be served more quickly and efficiently. This directory will be created within the Pretzel API server container, or if it is configured as a shared volume, then the resultsCache will be stored in the directory passed in. The benefit of this is that when the container is re-created, the resultsCache will be preserved. This is not essential, but will improve performance in particular for histograms where the chromosomes (Blocks) contain 1e5 - 1e7 features.
resultsCacheDir= # directory for results cache