# Usage

(installation)=
## Installation

### 🧠 Platform Notes

**Note:** This tool has been primarily tested on Linux-based systems, specifically Ubuntu 22.04.4 LTS. While it may run on other platforms, we recommend using a **Linux environment** for best compatibility and performance, especially for memory-intensive preprocessing steps such as **STAR** or **Cell Ranger** alignment.

>⚠️ **macOS users:** DOLPHIN is also compatible with macOS (Tested on macOS Ventura 13.0.1 with Apple M1, and Sequoia 15.3.2 with Apple M2 Pro), but **GPU acceleration is not supported** because CUDA is unavailable on this platform. All computations will run in **CPU-only mode**.

---

### 💻 Option 1: Linux Installation (Recommended)
📥 Step 1: Clone the Repository
```bash
git clone https://github.com/mcgilldinglab/DOLPHIN.git
cd DOLPHIN
```

🛠 Step 2: Create and Activate the Conda Environment
```bash
conda env create -f environment_linux.yaml
conda activate DOLPHIN
```

📦 Step 3: Install the DOLPHIN Python Package
```bash
pip install .
```

🧑‍💻 (Optional) Developer Mode Installation
```bash
pip install -e .
```

✅ Step 4: Validate the Installation
You can check if the package is correctly installed by opening Python and running:
```bash
import DOLPHIN.model
```
---

### 🍎 Option 2: macOS Installation (CPU-only)
Other steps are the same as in the Linux installation. Only Step 2 differs.
```bash
conda env create -f environment_mac.yaml
conda activate DOLPHIN
```

## Example Dataset
You can download the processed dataset from [One Drive.](https://mcgill-my.sharepoint.com/:f:/g/personal/kailu_song_mail_mcgill_ca/EvZtHeW7qjJJs_RHc2-327ABeLXafa-ruvfk9Vs134crig?e=kEPtAV)

**Required files**

For human alignment to the exon level, please download the pre-processed gtf file here:[One Drive.](https://mcgill-my.sharepoint.com/:f:/g/personal/kailu_song_mail_mcgill_ca/EvZtHeW7qjJJs_RHc2-327ABeLXafa-ruvfk9Vs134crig?e=kEPtAV)