BCCDC-PHL Auspice Docker Image

This repo contains a Dockerfile that can be used to build a container that runs Auspice, the web-based interactive phylogenetics application.

This Dockerfile is configured to build code from BCCDC-PHL/auspice, our fork of nextstrain/auspice.

Building the container

git clone git@github.com:BCCDC-PHL/auspice-docker.git

cd auspice-docker

docker build . -t bccdc-phl/auspice

Running the container

Prepare a datasets and narratives dir somewhere on the host filesystem:

mkdir -p /path/to/datasets

mkdir -p /path/to/narratives

Place any nextstrain dataset and narrative files there.

docker run -d\
  --name auspice \
  -p 4000:4000 \
  -v /path/to/datasets:/nextstrain/auspice/datasets \
  -v /path/to/narratives:/nextstrain/auspice/narratives \
  bccdc-phl/auspice

The application should be available on http://localhost:4000.

Pulling the Container from GitHub Container Registry

Pulling the container from the GitHub Container Registry (aka "GitHub Packages") requires a GitHub account and a personal access token.

First store the personal access token to an environment variable CR_PAT, then login to the container registry as follows:

export CR_PAT="ghp_a68fgN8..."
echo $CR_PAT | docker login ghcr.io -u <GITHUB_USERNAME> --password-stdin

The container can then be pulled as follows:

docker pull ghcr.io/bccdc-phl/auspice:release