Prerequisites

To run pipeline in docker, users need to be assigned corresponding server permissions. Please chat with Pengcheng, if you have this need.

How to run pipeline in Docker？

Once you have the permission, you can start the container with this command:

docker run -it pipeline:v2 /bin/bash

Then your terminal should start with something like:

app@ffa321300

Once you see this shown in your terminal, it indicates you are using the terminal of the running container. The string at the right of symbol '@' is the container ID, which often changes.

The default working directory of container is /home/app/cholera-mapping-pipeline, which contains these subfolders:

1. Analysis
2. Layers
3. packages

These folders contain all the necessary code for running pipeline and config files. To run the pipeline, type this command in the terminal:
Rscript Analysis/R/set_parameters.R -c Analysis/configs/<path_to_config.yml> Then the pipeline should be started. After running, the inputs for the Stan model will be saved at the Analysis/data