Use CDK to create Quilt packages from AWS HealthOmics
Use CDK to create and deploy the stack.
cp example.env .env # and edit
aws configure list-profiles # verify AWS credentials exist
npx npm install # if npm not present (but npx is)
npm install yarn -g # if yarn not present (but npm is)
yarn install
npx cdk bootstrap # if not yet done for this account/region
# start Docker if not already running
sudo systemctl start docker # e.g. on Linux (requires large Cloud9 instance!)
npm run deploy
You will also need to accept the Subscription from your email client.
Use your Quilt Catalog to browse the inputs and outputs
- Go to AWS Console and find the Omics-Quilt stack
- Copy names of the INPUT and OUTPUT buckets
- Copy the Status Topic ARN?!?
- Go your Quilt Catalog
- Click "+" on the front page (or Admin Settings -> Buckets)
- Click "+" in the upper right corner to add a new bucket
- Name: Physical Name from Stack
- Title: Omics Quilt Input / Output
- SNS Topic ARN
- Find or create your region's input parameters file:
./workflows/fastq/<region>.json
- Go to Console and find the input bucket
- Create Folders
fastq
and, inside that,<region>
- Upload the JSON file to
s3://<input-bucket>/fastq/<region>/<region>.json
TODO: Setup a Quilt package push that does this for you
- Go to the 'packager' Lambda and view the logs
- Grab the 'quilt+uri' from the output
- Paste into the URI field of the Quilt Catalog (next to the search bar)
- NOTE: May need to click the package name to stop page reloading
- Click "Expand" (and tripledot menu) to interact with result DataGrids
Uses pre-commit to pre-lint files.
pre-commit install
pre-commit run --all-files
Uses projen to manage project files.
yarn install
npm run projen
npm run eslint
npm run build
npm run test:watch