add documentation

RUN_INSTRUCTIONS.md

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+# Running on a Server
+
+This guide outlines the steps to set up and run **PatientX** on a server, including configuring a new installation directory, creating a virtual environment, and running the required scripts.
+
+---
+
+## 1. Creating a tmux Session (OPTIONAL but HIGHLY recommended)
+
+Please reference [`tmux` explanation documentation](WHY_TMUX.md) for more details on why to use `tmux`
+
+To create a new session, run
+
+```bash
+tmux new -s session_name
+```
+
+---
+
+## 2. SSH into HPC Cluster
+
+SSH into the HPC platform where you would like to run the PatientX code
+
+---
+
+## 3. Creating a Virtual Environment in Python
+
+Virtual environments are essential for managing dependencies and avoiding conflicts between different projects. This guide will walk you through creating and activating a virtual environment using `venv`.
+
+---
+
+### Prerequisites
+
+- Make sure Python 3.10+ is installed on your system. You can check by running:
+
+    ```bash
+    python --version
+    ```
+
+    or
+
+    ```bash
+    python3 --version
+    ```
+
+---
+
+### Creating a Virtual Environment
+
+Virtual environments can help us manage dependecies across projects and ensure there are no conflicting dependencies. To create a virtual environment, use the following command:
+
+```bash
+python -m venv {ENV_NAME}
+```
+
+This will create a new directory called myenv containing the virtual environment.
+
+---
+
+### Activating the Virtual Environment
+
+To activate the new virtual environment
+
+**On Windows**
+```powershell
+{ENV_NAME}\Scripts\Activate
+```
+
+**On macOS and Linux**
+```zsh
+source {ENV_NAME}/bin/activate
+```
+
+
+## 4. Installing Dependencies
+
+All dependecies and necessary packages for `PatientX.AI` can be installed by running
+
+```
+pip install -e .
+```
+
+---
+
+## 5. Start Ollama Server (optional - for LLM representation model)
+
+### Install Ollama
+
+Install [ollama](https://ollama.com/) by either going through their documentation or, if you do not have sudo access, by running
+```
+./script/install.sh
+```
+
+### Run Ollama Server
+
+Run ollama server in the background by running
+```bash
+ollama serve &
+```
+
+### Run LLM model
+Run the chosen model using
+```bash
+ollama run model-name &
+```
+
+---
+
+## 6. Run PatientX.AI Code
+
+To run the PatientX.AI code
+
+1. Update the config file with your desired parameters
+2. Run the pipeline using
+```bash
+python src/PatientX/run.py
+```
+3. For help, run
+```bash
+python src/PatientX/run.py --help
+```
+
+For further assistance, consult the **PatientX** documentation or contact the development team.

WHY_TMUX.md

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+# Tmux: Why Use It and How to Start a Session
+
+## Why Use Tmux?
+[Tmux (Terminal Multiplexer)](https://github.com/tmux/tmux/wiki) is a powerful tool that allows you to:
+
+- **Manage Multiple Terminal Sessions:** Run multiple shell sessions within a single window and easily switch between them.
+- **Persistent Sessions:** Keep your sessions running even after disconnecting, which is particularly useful for SSH connections. **This can be particularly useful here since running the full PatientX.AI may take some time depending on the size of the dataset and model configuration. Without `tmux`, if the ssh connection disconnects, the code may not run to completion**
+- **Efficient Workflow:** Split your terminal into multiple panes, allowing you to work on different tasks simultaneously.
+
+## Basic Tmux Commands
+
+### Start a New Session
+```bash
+tmux new -s session_name
+```
+This creates a new session named `session_name`.
+
+### Detach from a Session
+To detach from a session without stopping it, press:
+```
+Ctrl + b, then d
+```
+
+### List all Sessions
+To list all running sessions
+```
+tmux ls
+```
+
+### Reattach to an Existing Session
+To reattach to an existing session
+```
+tmux attach -t session_name
+```
+
+## Learn More
+
+For more details and advanced usage, refer to the [official tmux documentation](https://github.com/tmux/tmux/wiki)