Add post about adding jupyter kernel in EMBL's jupyterhub

content/posts/2022-03-02-jupyterhub-custom-kernel.md

+---
+date: 2022-03-02
+description:
+featured_image: "../images/2022-03-02/mockup-graphics-QOpX1O-Mcew-unsplash.jpg"
+tags: ["Renato Alves", "Bio-IT", "Community", "JupyterHub", "Kernel", "Jupyter"]
+title: "Adding and removing custom kernels to EMBL's JupyterHub"
+omit_header_text: true
+---
+
+# Jupyter kernels
+
+[Jupyter](https://jupyter.org/) is a server but also an ecosystem of tools for data exploration.  
+[JupyterLab](https://jupyterlab.readthedocs.io) is a web interface to notebooks which can be used to document, visualize and perform computations.  
+Computations in Jupyter are performed by a kernel, a separa component that understands how to perform calculations on request and return the result back to Jupyter.  
+
+As such, a single JupyterLab installation can have multiple kernels with different configurations for different needs.
+One can have a kernel for Python 3.8, another for 3.9 or 3.10, or even kernels from different languages such as R, Julia, or [many others](https://github.com/jupyter/jupyter/wiki/Jupyter-kernels).
+
+## Adding a kernel
+
+### Creating a new environment
+
+First start by creating a new environment with the software you need.  
+
+```sh
+conda create --prefix $HOME/conda-py310 python==3.10 jupyter seaborn
+source activate $HOME/conda-py310
+```
+
+In this case, `seaborn`. `jupyter` should also be installed so we can register the kernel with jupyterlab.
+
+### Installing/Removing the kernel
+
+```sh
+ipython kernel install --name "Py 3.10 local" --user
+```
+
+We can then confirm that the kernel was installed by issuing the following command:
+
+```sh
+jupyter kernelspec list
+```
+
+that will list all registered kernels:
+
+```
+Available kernels:
+  py-3.10-local    /home/ralves/.local/share/jupyter/kernels/py-3.10-local
+  python3          /home/ralves/conda-py310/share/jupyter/kernels/python3
+```
+
+If at any point we want to remove the kernel, we can use the listed name to remove it.
+For instance if we wanted to remove `py-3.10-local` that we added above we would:
+
+```sh
+jupyter kernelspec remove py-3.10-local
+```
+
+To confirm you can execute:
+
+```sh
+jupyter kernelspec list
+```
+that should list all but the removed kernel.
+```
+Available kernels:
+  python3          /home/ralves/conda-py310/share/jupyter/kernels/python3
+```
+
+If you then navigate to the dashboard of jupyterlab, what before looked like:
+
+![before](../../images/2022-03-02/initial_kernels_.png)
+
+will then become after a few minutes. If it still doesn't appear, refresh your browser.
+
+![after](../../images/2022-03-02/added_kernel.png)
+
+
+## Other languages
+
+As the jupyter ecosystem supports many languages, you can also install them on the EMBL jupyterhub system.  
+If you wanted to install typescript support, you need to install the `itypescript` kernel written for node.js 
+
+```sh
+conda create --prefix /home/ralves/conda-tjs "typescript=3.6"
+npm install -g itypescript
+```
+
+and then register it with jupyter
+
+```sh
+its --install=local --user
+```
+
+And like above, the new kernel should appear after a few minutes.
+
+
+## Who should I contact in case of issues?
+
+If you encounter any issues let us know in the [EMBL Bio-IT chat and channel](https://chat.embl.org).
+
+Renato Alves,  
+EMBL's JupyterDev team
+
+Photo by [Mockup Graphics](https://unsplash.com/@mockupgraphics)
+on [Unsplash](https://unsplash.com/s/photos/skill?utm_source=unsplash&utm_medium=referral&utm_content=creditCopyText)