For more information on how to use BINARY, please visit the official documentation.

BINARY Installation Guide

Follow these instructions to install BINARY, PySODB, and SOView in your Conda environment.

1. Extract BINARY installation package:

unzip BINARY.zip
cd BINARY/

2. Setup Conda Environment:

conda create -n binary python=3.8
conda activate binary

3. Install PyTorch with CUDA support:

Replace <torch_version> and <cuda_version> with the desired version.

pip install torch==<torch_version>+<cuda_version> -f https://download.pytorch.org/whl/<cuda_version>/torch_stable.html

Example:

pip install torch==1.13.0+cu117 -f https://download.pytorch.org/whl/cu117/torch_stable.html

4. Install PyTorch Geometric:

Visit the PyTorch Geometric Installation page(https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html) and then execute the copied command.

Example:

pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv torch_geometric -f https://data.pyg.org/whl/torch-1.13.0+cu117.html

5. Install additional Python packages:

pip install -r requirements.txt

6. Install mclust library:

conda install -c r rpy2

Then, set the R environment variables. Replace <user_name> and <environment_name> with appropriate values:

export R_HOME=/home/<user_name>/anaconda3/envs/<environment_name>/lib/R
export R_LIBS_USER=/home/<user_name>/anaconda3/envs/<environment_name>/lib/R/library

When configuring the installation paths for R_HOME and R_LIBS_USER, the standard Linux and Conda environment paths (such as .conda) may not be applicable. In such cases, users need to locate the R path and library path within the Conda virtual environment's Python packages and replace them accordingly.

Now, install the mclust library using Python:

python -c "import rpy2.robjects.packages as r; utils = r.importr('utils'); package_name = 'mclust'; utils.install_packages(package_name)"

7. Install PySODB:

Keep the binary conda environment active and execute:

git clone https://github.com/TencentAILabHealthcare/pysodb.git
cd pysodb/
python setup.py install

8. Install SOView:

git clone https://github.com/yuanzhiyuan/SOView.git
cd SOView/
pip install .