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.
git clone [email protected]:BCCDC-PHL/auspice-docker.git
cd auspice-docker
docker build . -t bccdc-phl/auspice
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 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