scGPT环境安装

scGPT环境安装

conda create -n scgpt_2
conda activate scgpt_2
conda install python=3.10.11 cudatoolkit=11.7 cudatoolkit-dev 'gxx>=6.0.0,<12.0' cudnn -c conda-forge
pip install torch==1.13.0+cu117 torchvision==0.14.0+cu117 torchaudio==0.13.0 --extra-index-url https://download.pytorch.org/whl/cu117
pip install packaging
pip install flash-attn==1.0.4 --no-build-isolation
conda install r-base r-devtools
pip install --no-deps scgpt
pip install ipykernel
python -m ipykernel install --user --name=scgpt_2
pip install pandas
pip install scanpy
pip install scvi-tools
pip install numba --upgrade
pip install numpy==1.24.4
pip install torchtext==0.14.0
pip install scib
pip install datasets==2.14.5 transformers==4.33.2

我按照以上教程成功应用于A6000，其他安装教程参考https://github.com/bowang-lab/scGPT/issues/153#issuecomment-1950228683