Infrastructure provisioning for 4dn-dcic AWS environments, using Cloudformation
See docs/setup.rst.
poetry update # only if updates are needed, kept in poetry.lock
poetry install
To make stack changes, see docs/making_stack_changes.rst. To create a new stack, see docs/create_new_stack.rst.
To deploy from scratch, see docs/deploy_new_account.rst.
Validate Legacy Configuration:
make legacy
Validate Alpha Configuration:
make alpha
To lint a template:
cfn-lint path/to/template
To get help:
poetry run cli -h
See docs/.
For an in-depth overview, see docs/architecture.rst.
Once the ECS Service has come online, the portal should be accessible from the URL output from the ECS Stack. At this point we are ready to start testing the portal functionality by loading a demo case. Some important caveats of the current test setup:
- Further customization is needed to run this on new environments. Full customization out of the box is still TODO.
- Bioinformatics analysis is completely mocked out (an output VCF is uploaded immediately).
- It may take a few hours for this process to run, especially if it is the first time.
Instructions for testing: (TODO: May need some updating)
# First load required knowledge base data
make load-knowledge-base
# Then perform metadata bundle submission
make submission
# Then, after following the "make submission" output instructions
# queue output VCF ingestion
make ingestion
foursight_development contains scripts for running foursight checks and actions for
development purposes as well as a separate app configuration (development_app.py) than
the one used for deployment.
For more information, see docs/running_foursight_from_ec2.rst.