diff --git a/README.md b/README.md index c925803..8905713 100644 --- a/README.md +++ b/README.md @@ -8,19 +8,40 @@ You can run the notebooks locally (please note: the Anaconda Python enviornment 1. Install Anaconda to manage virtual environments. You can follow the instructions [here](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) 2. Clone the repository and get into the repo folder: ``` - git clone https://github.com/SARScripts/SInCohMap - cd SInCohMap +git clone https://github.com/SARScripts/SInCohMap +cd SInCohMap ``` 3. Create a new conda environment with the following command: ``` - conda env create -f environment.yml +conda env create -f environment.yml ``` 4. Once the process is complete, you can activate the environment: ``` - conda activate sincohmap +conda activate sincohmap ``` 5. Now you can start the Jupyter Notebook Server and use the notebooks, just typing: ``` - jupyter notebook +jupyter notebook ``` 6. This should open up a new window in your default web browser, where you can select the notebook you prefer. + +### Using an existing Jupyter instance + +If there is already a Jupyter instance (i.e. the JupyterHub offered by Eurac Research), you can add the kernel from the newly created conda environment without running another one. +The necessary additional steps are: +``` +$ conda activate sincohmap +(sincohmap)$ conda install ipykernel +(sincohmap)$ ipython kernel install --user --name=sincohmap +(sincohmap)$ conda deactivate +``` +Source: [stackoverflow](https://stackoverflow.com/questions/53004311/how-to-add-conda-environment-to-jupyter-lab) + +Please note: if your console does not recognize the `conda` command, you need to initialize it before running the previous commands, using: +`$ conda init bash` + +Now the new kernel should be available in your Jupyter Lab. To use the new kernel: +1. Click on the kernel selector in the upper right corner of the page +2. Select the new kernel +3. Restart the kernel +![image](https://user-images.githubusercontent.com/31700619/150111234-6cf44258-5fc1-4746-837a-7884fb8939c3.png)