Updating scgpt #29
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Updating scgpt #29
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rcannood
approved these changes
Oct 19, 2025
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| git clone https://github.com/bowang-lab/scGPT && \ | ||
| pip install torch==2.2.0 torchvision==0.17.0 torchaudio==2.2.0 --index-url https://download.pytorch.org/whl/cu121 && \ | ||
| pip install "flash-attn<1.0.5" --no-build-isolation && \ | ||
| pip install ipykernel pandas scanpy numba "numpy<1.24" torchtext==0.17.0 scib "scvi-tools<1.0" datasets==2.14.5 transformers==4.33.2 wandb "cell-gears<0.0.3" torch_geometric pyarrow==15.0.0 gdown && \ | ||
| cd scGPT && pip install -e . --no-deps |
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this aligns with how we install scgpt in the batch integration task and seems to work
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Describe your changes
moving this to a new PR