Installation#
Overview#
There are three ways to install OpenSpliceAI: via pip, through conda, or from source. OpenSpliceAI requires Python 3.9 or higher and depends on several third‐party packages, including:
PyTorch – used for deep learning model training and inference. See the PyTorch website for more details.
mappy – provides Python bindings for minimap2, enabling fast genomic alignments. Visit its page on PyPI for further information.
Prerequisites#
Python: Version 3.9 or higher.
Ensure that your system has the necessary compilers.
For GPU acceleration (when using PyTorch), install the required NVIDIA drivers and CUDA toolkit:
NVIDIA GPU Drivers: Visit the official NVIDIA Driver Downloads page:
CUDA Toolkit: Download the latest CUDA Toolkit from the official CUDA downloads page. For detailed installation instructions, please refer to the CUDA Installation Guide.
Installation Methods#
Install through pip#
OpenSpliceAI is available on PyPI. Pip automatically resolves and installs all required dependencies.
pip install openspliceai
This command installs third‐party libraries including:
Software dependency
python >= 3.9.0
h5py >= 3.9.0
numpy >= 1.24.4
gffutils >= 0.12
pysam >= 0.22.0
pandas >= 1.5.3
pyfaidx >= 0.8.1.1
tqdm >= 4.65.2
torch >= 2.2.1
torchaudio >= 2.2.1
torchvision >= 0.17.1
scikit-learn >= 1.4.1.post1
biopython >= 1.83
matplotlib >= 3.8.3
matplotlib-inline >= 0.1.7
psutil >= 5.9.2
Version Warning
If your numpy version is >= 1.25.0, it requires Python >= 3.9. For further guidance, please refer to the scientific python ecosystem coordination guideline SPEC 0.
Install through conda#
Installing via conda is the easiest way to set up a sandboxed environment with all dependencies.
conda install -c bioconda openspliceai
This command installs OpenSpliceAI and its dependencies, including PyTorch and mappy. To install or update these packages individually, you can use:
For PyTorch:
# CPU-only version (Conda packages are no longer available):
pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
# For GPU support (Conda packages are no longer available):
pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu126
For mappy:
conda install -c bioconda mappy
Install from source#
Alternatively, install OpenSpliceAI from source by cloning the GitHub repository:
git clone https://github.com/Kuanhao-Chao/OpenSpliceAI.git
cd OpenSpliceAI
python setup.py install
Detailed Installation for PyTorch and mappy#
PyTorch:
Recommended Version: 2.2.1 or later.
Usage: Essential for model training and inference in OpenSpliceAI.
Installation Tips:
For GPU acceleration, ensure your NVIDIA drivers and CUDA toolkit are installed.
Visit the PyTorch official site to select the appropriate command for your operating system.
mappy:
Recommended Version: 2.28.
Usage: Provides Python bindings for minimap2 for rapid genomic alignments.
Installation Tips:
To install via pip:
pip install mappy
Or via conda:
conda install -c bioconda mappy
For advanced usage (e.g., multithreading), refer to the mappy GitHub repository or the Bioconda mappy recipe.
Check OpenSpliceAI Installation#
After installing, verify that OpenSpliceAI is properly set up by running:
openspliceai -h
You should see the usage information and version details printed in your terminal.
Terminal Output Example#
Next Steps#
Once installation is complete, please proceed to the Quick Start Guide to begin working with OpenSpliceAI for data creation, model training, prediction, calibration, and variant analysis.
