Usage

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.

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💻 Option 1: Linux Installation (Recommended)

📥 Step 1: Clone the Repository

git clone https://github.com/mcgilldinglab/DOLPHIN.git
cd DOLPHIN

🛠 Step 2: Create and Activate the Conda Environment

conda env create -f environment_linux.yaml
conda activate DOLPHIN

📦 Step 3: Install the DOLPHIN Python Package

pip install .

🧑‍💻 (Optional) Developer Mode Installation

pip install -e .

✅ Step 4: Validate the Installation You can check if the package is correctly installed by opening Python and running:

import DOLPHIN.model

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🍎 Option 2: macOS Installation (CPU-only)

Other steps are the same as in the Linux installation. Only Step 2 differs.

conda env create -f environment_mac.yaml
conda activate DOLPHIN

Example Dataset

You can download the processed dataset from One Drive.

Required files

For human alignment to the exon level, please download the pre-processed gtf file here:One Drive.