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zhoux85 / STAligner

STAligner is a tool for alignment and integration of spatially resolved transcriptomics data.
MIT License
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Can't install Python environment for STAligner #2

Closed vladimirkovacevic closed 1 year ago

vladimirkovacevic commented 1 year ago

requirements.txt is missing versions of the libraries. I also tried versions from requirements.txt of the forked repository it also gives an error on import STAligner that torch_sparse is missing and when I install it gives:

OSError: /home/ubuntu/anaconda3/envs/STAligner/lib/python3.8/site-packages/torch_sparse/_diag_cpu.so: undefined symbol: _ZN3c106detail19maybe_wrap_dim_slowEllb

Ubuntu 22.04.1 LTS

zhoux85 commented 1 year ago

Hi. With the following PyTorch and PyG versions, I import STAligner successfully. cuda 11.6 torch 1.12.0 torch-geometric 2.2.0 torch-scatter 2.1.0 torch-sparse 0.6.16

or

cuda 11.1 torch 1.9.1 torch-geometric 2.0.3 torch-scatter 2.0.9 torch-sparse 0.6.12

I installed PyTorch and PyG with the guidelines from

https://github.com/pyg-team/pytorch_geometric#installation

pip install "https://download.pytorch.org/whl/cu113/torch-1.12.0%2Bcu113-cp38-cp38-linux_x86_64.whl"
pip install pyg_lib torch_scatter torch_sparse -f https://data.pyg.org/whl/torch-1.12.0+cu113.html
pip install torch_geometric

Hope this helps.

vladimirkovacevic commented 1 year ago

I managed to install cuda 11.7 and pytorch 1.13 on AWS machine g5.8xlarge. All the examples from the tutorials worked. Run into some issues with running mouse embryos from MOSTA, I'll create a new issue for consistency.