Setup

Scripts to set up a minimal system with required tools for CageLab / Opticka.

Clone this repo, cd to this folder, then run bootstrap.sh to install the required tools and set up the environment.

This installs netbird, nomachine, x-cmd, pixi and pixi installs python and other command line tools needed by AWS CLI for Alyx. There is an option to install MATLAB using the very cool mpm (MATLAB Package Manager) if you have a license.

Instructions for how to setup secure remote login with netbird, SSH and NoMachine: https://cogplatform.github.io/Notes/src/RemoteLogin.html

Critical tools:

1. Netbird is used for network access.
2. SSH and NoMachine is used for remote access/desktop, tunneled only through Netbird. Both SSH and NoMachine are setup to use SSH keys only, no passwords.
3. MATLAB R2025a (see also mpm).
4. https://pixi.sh as a cross-platform package manager for other tools.
5. x-cmd for shell management, especially setting up chinese mirrors etc.
6. awscli is used to upload data to data server for Alyx.
7. Python with a specific version (V3.11 is needed for MATLAB R2024a) to use awscli. https://mathworks.com/support/requirements/python-compatibility.html
8. Java is used for matlab-jzmq, and needs to be a specific version (V17 for MATLAB 2025a). https://mathworks.com/support/requirements/openjdk.html

TODO

We need to package cogmoteGO (possibly as a Conda package so we can install it with Pixi).