How to automatically create a environment.yml that works with repo2docker

This how-to explains how to create a environment.yml that specifies all installed packages and their precise versions from your environment.

The challenge

conda env export -f environment.yml creates a strict export of all packages. This is the most robust for reproducibility, but it does bake in potential platform-specific packages, so you can only use an exported environment on the same platform.

repo2docker uses a linux based image as the starting point for every docker image it creates. However a lot of people use OSX or Windows as their day to day operating system. This means that the environment.yml created by a strict export will not work with error messages saying that certain packages can not be resolved (ResolvePackageNotFound).

The solution

Follow this procedure to create a strict export of your environment that will work with repo2docker and sites like

We will launch a terminal inside a basic docker image, install the packages you need and then perform a strict export of the environment.

  1. install repo2docker on your computer by following Installing repo2docker
  2. in a terminal launch a basic repository repo2docker inside repo2docker
  3. open the URL printed at the end in a browser, the URL should look like
  4. open a terminal by clicking “New -> Terminal” next to the “Upload” button on the right hand side of the webpage
  5. install the packages your project requires with conda install <yourpackages>
  6. use conda env export -n root to print the environment
  7. copy and paste the environment you just printed into a environment.yml in your projects repository
  8. close your browser tabs and exit the repo2docker session by pressing Ctrl-C.

This will give you a strict export of your environment that precisely pins the versions of packages in your environment based on a linux environment.