Docker

{EpiNow2} was developed in a docker container based on the rocker/geospatial docker image. A bash script version of these instructions is available here for linux.

To build the docker image run (from the EpiNow2 directory):

docker build . -t epinow2

Alternatively to use the prebuilt image first login into the GitHub package repository using your GitHub credentials (if you have not already done so) and then run the following:

# docker login docker.pkg.github.com
docker pull docker.pkg.github.com/epiforecasts/epinow2/epinow2:latest
docker tag docker.pkg.github.com/epiforecasts/epinow2/epinow2:latest epinow2

To run the docker image run:

docker run -d -p 8787:8787 --name epinow2 -e USER=epinow2 -e PASSWORD=epinow2 epinow2

The rstudio client can be found on port :8787 at your local machines ip. The default username:password is epinow2:epinow2, set the user with -e USER=username, and the password with - e PASSWORD=newpasswordhere. The default is to save the analysis files into the user directory.

To mount a folder (from your current working directory - here assumed to be tmp) in the docker container to your local system use the following in the above docker run command (as given mounts the whole epinow2 directory to tmp).

--mount type=bind,source=$(pwd)/tmp,target=/home/epinow2

To access the command line run the following:

docker exec -ti epinow2 bash