Docker Commands

The Docker Compose file for the project contains five services, which are grouped into profiles. To simplify we’ve developed a Makefile.

In order to rebuild the images for any of these commands, subsitute run for build.

The Makefile contains several commands meant to make life easier:

Clean old images and containers:

make clean

Note

• Removes all images and stagnant containers

• Use with caution

Preprocess new sequencing data:

make run-new-data

Note

• Uses Bjorn to get .fasta and metadata files from a GitHub repo and preprocesses data for downstream use

• Make sure you’ve modified the bjorn config file and changed the docker-compose.yml bind parameter as documented in Parameters an Data Formatting

Ingest data into ElasticSearch and then bring the website up:

make run-ingest

Note

• Ingests preprocessed data into ElasticSearch, and brings up the ElasticSearch database, tornado server, and client side.

• Will overwrite a prior ElasticSearch index

• If zipcode visualizations are wanted, .geojson file must be provided prior to this step

Bring the website up without adding or preprocessing data:

make run-website

Note

• Brings up the ElasticSearch database, tornado server, and client side

Run only ElasticSearch data ingest:

make run-ingest-only

Note

• Runs the container that ingests data into ElasticSearch, assumes that ElasticSearch is already running

• Our use case for this is updating the data without shutting down the website

Run all the services:

make run-website

Note

• Runs bjorn to preprocess data, ingests data into ElasticSearch, brings up the ElasticSearch database, tornado server, and client side