Getting Started

Overview

Install
Format data
Modify configuration parameters
Run docker command

Installation

Clone The Repository

To install outbreak.network local build first clone the repository from GitHub.

git clone git@github.com:andersen-lab/outbreak.info.git

Populate the Submodules

Outbreak local contains two submodules bjorn and outbreak-api-lite. Make sure the submodules are populated by navigating to the appropriate folders and running the following:

git submodule update --init --recursive

Formatting Data

All data needs to be appropriately formatted including:

Github repository structure for .fasta files and associated metadata.
Zipcode .geojson file if provided.

The Parameters an Data Formatting describes these formats in detail.

Modify Parameter Configuration

Two parameter configuration files exist within outbreak.info local.

Example parameters for running Bjorn are located here.
Example parameters for everything else are located here.

Prior to executing any commands, these files will need to be filled out appropriately. The Parameters an Data Formatting section describes each value in detail.

Run a Docker Command

Each major step (Bjorn, ElasicSearch Ingestion, ElasticSearch, Tornado, and Client) is defined as a service in the docker-compose.yml. The Makefile allows for easy running of groups of services. Example commands to run Makefile profiles can be found Docker Commands.