docker

How to reproduce this manuscript's application environment

Docker

To preserve the application environment (e.g. Python, R, specific package versions) used in this project, we define it as a Docker container image. By also using this container definition (on an x86_64 CPU) you can replicate our environment.

Setup

Install Docker if you have not already.

Build the container image in this directory with:

cd animal_tree_root/docker
docker build -t animal_tree_root .

Docker will automatically look for a recipe file called Dockerfile in this directory and build the container image for you, tagging it as animal_tree_root.

Running analyses

The manuscript was written in R Markdown. You can start an RStudio Server session to examine it and its environment:

# change /path/to/animal_tree_root to the location of this repo on your computer
docker run --rm  -dP -e PASSWORD=secret123 -e USERID=$UID -v /path/to/animal_tree_root:/animal_tree_root -p 8787:8787 animal_tree_root

Then go to http://localhost:8787/ in your browser. Log in with username: rstudio and password: secret123 . You can jump to the repo's R directory with the R command:

setwd("/animal_tree_root/manuscript")

To start an interactive shell for running other analyses (e.g. those in /animal_tree_root/reconciliation/scripts):

# change /path/to/animal_tree_root to the location of this repo on your computer
docker run --rm -it -e USERID=$UID -v /path/to/animal_tree_root:/animal_tree_root animal_tree_root bash