Rethink database to support real-time virus analysis

Introduction

The nextstrain project is an attempt to make flexible informatic pipelines and visualization tools to track ongoing pathogen evolution as sequence data emerges. The nextstrain project derives from nextflu, which was specific to influenza evolution.

nextstrain is comprised of three components:

  • fauna: database and IO scripts for sequence and serological data
  • augur: informatic pipelines to conduct inferences from raw data
  • auspice: web app to visualize resulting inferences

fauna

Definition: The animals of a given region or period considered as a whole. Also, prophetic Roman deity.

The fauna database stores viral sequences and serological data in rethinkdb. The current database and scripts is designed around influenza and Zika viruses.

vdb

The virus database (vdb) is used to store viral information in an organized schema. This allows easy storage and querying of viruses which can be downloaded in formatted fasta or json files.

tdb

The titer database (tdb) is used to store titer measurements in an organized schema. This allows easy storage and downloading of all measurements in the database.

Install

Clone the repo and load submodules:

git clone https://github.com/nextstrain/fauna.git
git submodule update --init --recursive

Install Python modules needed to run upload/download scripts:

pip install -r requirements.txt

Install Chateau Web UI:

npm install

Backup and restore functionality requires the rethinkdb command line utility. This can be installed by following instructions here. With Homebrew, you can just do:

brew install rethinkdb

Chateau

Chateau allows easy web access to the database. To run, do the following:

For remote rethink instance

  1. Set environment variables RETHINK_HOST and RETHINK_AUTH_KEY.
  2. Run with npm run chateau from directory fauna/.
  3. Go to http://localhost:3000/.

For local rethink instance

  1. Run with npm run chateau-local from directory fauna/.
  2. Go to http://localhost:3001/.

Chateau configurations are stored in config.js for remote server and config_local.js for local server.

Docker

Build a Docker image for fauna:

docker build -t nextstrain/fauna:latest .

Push image to the Docker Hub:

docker push nextstrain/fauna:latest

Run a shell from within the container:

docker run --env-file environment_docker.env -t -i nextstrain/fauna /bin/bash

License and copyright

Copyright 2016 Trevor Bedford and Charlton Callender.

Source code to nextstrain is made available under the terms of the GNU Affero General Public License (AGPL). nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.