Cavatica Integration¶

The Study Creator may integrate with Cavatica to automate the setup of new projects for bioinformatics work.

Feature Flags¶

The Cavatica integration features may enabled with the following feature flags.

FEAT_CAVATICA_CREATE_PROJECTS¶: Create new projects in Cavatica when new studies are created

FEAT_CAVATICA_COPY_USERS¶: New analysis projects created by the study creator will have users copied over from a template project supplied by the CAVATICA_USER_ACCESS_PROJECT setting.

FEAT_CAVATICA_MOUNT_VOLUMES¶: New Cavatica projects will have the study’s bucket attached as a volume upon creation.

Configuration Settings¶

The following settings need to be provided in order for the Cavatica integration to function correctly.

CAVATICA_URL¶

default: https://cavatica-api.sbgenomics.com/v2

The url of the Cavatica api endpoint

CAVATICA_HARMONIZATION_ACCOUNT¶

required

The username for the Cavatica account associated with the token given by CAVATICA_HARMONIZATION_TOKEN.

CAVATICA_HARMONIZATION_TOKEN¶

required

The api token for the harmonization Cavatica account

CAVATICA_DELIVERY_ACCOUNT¶

required

The username for the Cavatica account associated with the token given by CAVATICA_DELIVERY_TOKEN.

CAVATICA_DELIVERY_TOKEN¶

required

The api token for the delivery Cavatica account

CAVATICA_DEFAULT_WORKFLOWS¶

default: Empty string

example: bwa-mem gatk-haplotypecaller

A space separated list of the workflow projects to set up for a new study

CAVATICA_USER_ACCESS_PROJECT¶

default: kids-first-drc/user-access

The project_id of a Cavatica project which contains users and permissions that will be copied over to new Cavatica analysis projects.

CAVATICA_READ_ACCESS_KEY¶

default: None

The AWS access key for a read-only user with priviledges for the study buckets.

CAVATICA_READ_SECRET_KEY¶

default: None

The AWS secret key for a read-only user with priviledges for the study buckets.

CAVATICA_READWRITE_ACCESS_KEY¶

default: None

The AWS access key for a user with priviledges for the study buckets.

CAVATICA_READWRITE_SECRET_KEY¶

default: None

The AWS secret key for a user with priviledges for the study buckets.

Configuration¶

To utilize the Cavatica features, the Study Creator needs to be provided with Cavatica developer tokens. To get a Cavatica token, log in / sign up into Cavatica , and navigate to the developer page. Export the token under CAVATICA_HARMONIZATION_TOKEN and CAVATICA_DELIVERY_TOKEN in the Study Creator’s environment to allow it to utilize the tokens to communicate with Cavatic. These settings may also take different tokens, if each project type should utilize different Cavatica accounts.

Operation¶

When a new study is created via the createStudy mutation, the Study Creator will work with Cavatica to set up new projects for future bioinformatics work. This includes: - Specifying a standard project id format - Naming the project based on the Study’s name - Copying the description from that of the study’s - Creating harmonization projects for each desired workflow

Cavatica Accounts¶

The Study Creator creates two different kinds of projects: harmonization and delivery. It offers the ability to create each type within its own distinct account by providing CAVATICA_HARMONIZATION_TOKEN and CAVATICA_DELIVERY_TOKEN settings. If the separation of the two projects types is not needed, both settings may be configured to share the same token.

Synchronizing Projects¶

The Study Creator provides the syncProjects mutation which will iterate all projects for both cavatica tokens and ensure that all the projects within the Study Creator exist and are up to date. This is a purely passive operation meaning that no data will be updated in Cavatica, only in the Study Creator’s view of the projects.

Volume Mounting¶

A bucket will be created for new studies as part of the study creation flow given that FEAT_BUCKETSERVICE_CREATE_BUCKETS is enabled. This bucket may optionally be added as a volume during the study creation flow by enabling FEAT_CAVATICA_MOUNT_VOLUMES and providing S3 credentials in the configuration given with the CAVATICA_READWRITE_ACCESS_KEY and CAVATICA_READWRITE_SECRET_KEY key-pair.

The new Cavatica volume will be added to the account of the token given by CAVATICA_HARMONIZATION_TOKEN with full privileges and the account specified by CAVATICA_DELIVERY_ACCOUNT will be added as a user with read and copy permissions.