The required packages can be installed using pip:

pip install -r requirements.txt

Note:

R and the metafor package are both needed to fit the mixed-effect model in meta-analysis.ipynb through the package rpy2. Alternatively, you can use the conda environment described in environment.yml.

If you have Docker installed on your computer and running, you can run the code in the same environment described in this repository using repo2docker.

1. Simply install repo2docker from pyPI:

pip install jupyter-repo2docker

2. Run the following command in your terminal:

jupyter-repo2docker https://github.com/neurolibre/myelin-meta-analysis

After building (it might take a while!), it should output in your terminal something like:

Copy/paste this URL into your browser when you connect for the first time,
    to login with a token:
        http:https://0.0.0.0:36511/?token=f94f8fabb92e22f5bfab116c382b4707fc2cade56ad1ace0

This should start a Jupyter session on your browser and make all the resources you see when you launch a Binder for this repository.

To re-use your container built by repo2docker, do the following:

1. Run docker images command and copy the IMAGE ID to your clipboard
2. Run the following command to start the container:

docker run -it --rm -p 8888:8888 `PASTE IMAGE ID HERE` jupyter notebook --ip 0.0.0.0

You can use Interact Inline or Launch in Binder buttons at the top of each page of the Jupyter Book.

Alternatively, you can start a Binder session by clicking the badge below: