tobylanser / cell2fate Goto Github PK

The standard recommended workflow for using cell2fate can be found in this this tutorial here. For further notebooks and examples including more datasets and integration with cell2location we have more notebooks here

We suggest using a separate conda environment for installing cell2fate.

Create a conda environment and install the cell2fate package.

git clone https://github.com/tobylanser/cell2fate
cd cell2fate
conda env create --name cell2fate_env --file=environment.yml


conda activate cell2fate_env

conda install pytorch==1.11.0 cudatoolkit==11.3 -c pytorch

pip install git+https://github.com/tobylanser/cell2fate

To use this environment in a jupyter notebook, add a jupyter kernel for this environment:

conda activate cell2fate_env
python -m ipykernel install --user --name=cell2fate_env --display-name='Environment (cell2fate_env)'

If you do not have conda please install Miniconda first:

cd /path/to/software
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
# use prefix /path/to/software/miniconda3

Before installing cell2fate and it's dependencies, it could be necessary to make sure that you are creating a fully isolated conda environment by telling python to NOT use user site for installing packages, ideally by adding this line to your ~/.bashrc file , but this would also work during a terminal session:

export PYTHONNOUSERSITE="someletters"