Real-time tracking of influenza evolution

Command notes

Remove all containers

docker rm `docker ps --no-trunc -aq`

Remove all images (careful)

docker rmi $(docker images -q)

Build

Build vdb

From within the vdb/ directory

Build vdb docker image

docker build -t trvrb/vdb:latest .

Build augur

From within the nextflu/augur/ directory

Build augur docker image

docker build -t trvrb/augur:latest .

Push image to hub

docker push trvrb/augur:latest

Build auspice

From within the nextflu/auspice/ directory

Build auspice docker image

docker build -t trvrb/auspice:latest .

Push image to hub

docker push trvrb/auspice:latest

Run

Setup

Create a named data volume for augur-data

docker create --name augur-data -v /Users/trvrb/Dropbox/current-projects/nextstrain/augur/data:/nextflu/augur/data trvrb/augur

Create a named data volume for auspice-data

docker create --name auspice-data -v /Users/trvrb/Dropbox/current-projects/nextstrain/auspice/data:/nextflu/auspice/data trvrb/auspice

Augur

From within the nextflu/augur/ directory, run a shell from within the container

docker run -t -i --volumes-from augur-data --volumes-from auspice-data trvrb/augur /bin/bash

Run augur

docker run --volumes-from augur-data --volumes-from auspice-data trvrb/augur

Run shell

docker run -t -i --volumes-from augur-data --volumes-from auspice-data trvrb/augur /bin/bash

Auspice

From within the nextflu/auspice/ directory, run a shell from within the container

docker run -t -i --volumes-from auspice-data -p 4000:4000 trvrb/auspice /bin/bash

Run auspice

docker run --volumes-from auspice-data -p 4000:4000 trvrb/auspice