Real-time tracking of influenza evolution

Docker

Previously, we had been using Docker to provide portability of the build process. Currently Nextflu is built with augur and portability is provided through janus. Docker functionality is deprecated.

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