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step-by-step-installation.md

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Step-by-step guide to create conda environment

  • Create a new conda environment with the name myenv and python version 3.7
conda create -n marker python=3.8 ipython jupyter
  • Activate the environment
conda activate myenv
  • Install Pytorch
conda install pytorch==1.13.1 torchvision==0.14.1 torchaudio==0.13.1 pytorch-cuda=11.7 -c pytorch -c nvidia
  • Install PyTorch-Lightning
pip install pytorch-lightning==1.5.8
  • Install Scanpy and dependencies
conda install -c conda-forge scanpy python-igraph leidenalg
  • Install torch geometric
pip install torch_geometric
pip install --no-index torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-1.13.1+cu117.html
  • Install scikit-misc
pip install --user scikit-misc
  • Install rpy2 for mclust clustering
conda install -c conda-forge rpy2

Now, you have successfully set up the Conda environment for STAMarker. Make sure to activate the environment whenever you work on your project using the following command:

conda activate marker