# Setup

**Repository Path**: CogPlatform/Setup

## Basic Information

- **Project Name**: Setup
- **Description**: Setup scripts for CageLab devices
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: main
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2025-05-13
- **Last Updated**: 2025-10-09

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# 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](https://netbird.io) is used for network access.
2. SSH and [NoMachine](https://www.nomachine.com) 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)](https://www.mathworks.com/products/mpm.html).
5. <https://pixi.sh> as a cross-platform package manager for other tools.
4. [x-cmd](https://www.x-cmd.com) for shell management, especially setting up chinese mirrors etc.
1. `awscli` is used to upload data to data server for Alyx.
1. `Python` with a specific version (V3.11 is needed for MATLAB R2024a) to use awscli. <https://mathworks.com/support/requirements/python-compatibility.html>
1. `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).