scGPT

GitHub: https://github.com/bowang-lab/scGPT

The procedures are posted on scGPT site, https://github.com/bowang-lab/scGPT/issues/306.

The installation is done as follows (scGPT.sh with additional verification inside Python),

module load python/3.11.0-icl
python -m venv scGPT-models
source scGPT-models/bin/activate
pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu117
pip install packaging
pip install ipykernel
pip install scgpt flash-attn==1.0.4
pip uninstall numpy -y
pip install numpy==1.25.2
pip install scvi-tools==0.20.3 anndata==0.9.2 scanpy==1.9.3
pip install wandb
pip install faiss-cpu
pip install nbformat
pip list | awk '/scanpy|scib|scvi|scgpt|flash-attn|torch|wandb/'

As it happens, numpy 2.1.2 causes issues with scvi-tools and a compatible one is chosen.

flash-attn              1.0.4
pytorch-lightning       1.9.5
scanpy                  1.9.3
scgpt                   0.2.4
scib                    1.1.7
scvi-tools              0.20.3
torch                   2.0.1+cu117
torchaudio              2.0.2+cu117
torchdata               0.6.1
torchmetrics            1.7.0
torchtext               0.15.2
torchvision             0.15.2+cu117
wandb                   0.19.9

A separate attempt to use a released version is made but appears to have issues with anndata and mudata, which is resolved by mirroring modules (mudata==0.2.3 and anndata==0.9.2) and the trick for torch, etc. as above.

module load python/3.9.12/gcc/pdcqf4o5
python -m venv scGPT-release
source scGPT-release/bin/activate
wget -qO- https://github.com/bowang-lab/scGPT/archive/refs/tags/v0.2.4.tar.gz | tar xvfz -
cd scGPT-0.2.4/
pip install -e .
pip install ipykernel
pip install gseapy
pip install torch.geometric
pip install einops
pip list
pip uninstall torch -y
pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu117
pip install flash-attn==1.0.4
pip uninstall numpy -y
pip install numpy==1.25.2
pip install wandb
pip install iprogress
pip install nbformat
pip list | awk '/scanpy|scib|scvi|scgpt|flash-attn|torch|wandb/'

giving

flash-attn               1.0.4
pytorch-lightning        1.9.5
scanpy                   1.10.3
scib                     1.1.7
scvi-tools               0.20.3
torch                    2.0.1+cu117
torch-geometric          2.6.1
torchaudio               2.0.2+cu117
torchmetrics             1.7.1
torchvision              0.15.2+cu117
wandb                    0.19.9