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+# Installation
+
+NicheCompass is available for Python 3.9. It does yet not support Apple silicon.
+
+
+We do not recommend installation on your system Python. Please set up a virtual
+environment, e.g. via conda through the [Mambaforge] distribution, or create a
+[Docker] image.
+
+## Additional Libraries
+
+To use NicheCompass, you need to install some external libraries. These include:
+- [PyTorch]
+- [PyTorch Scatter]
+- [PyTorch Sparse]
+- [bedtools]
+
+We recommend to install the PyTorch libraries with GPU support. If you have
+CUDA, this can be done as:
+
+```
+pip install torch==${TORCH}+${CUDA} --extra-index-url https://download.pytorch.org/whl/${CUDA}
+pip install pyg_lib torch_scatter torch_sparse -f https://data.pyg.org/whl/torch-${TORCH}+${CUDA}.html
+```
+where `${TORCH}` and `${CUDA}` should be replaced by the specific PyTorch and
+CUDA versions, respectively.
+
+For example, for PyTorch 2.0.0 and CUDA 11.7, type:
+```
+pip install torch==2.0.0+cu117 --extra-index-url https://download.pytorch.org/whl/cu117
+pip install pyg_lib torch_scatter torch_sparse -f https://data.pyg.org/whl/torch-2.0.0+cu117.html
+```
+
+To install bedtools, you can use conda:
+```
+conda install bedtools=2.30.0 -c bioconda
+```
+
+Alternatively, we have provided a conda environment file with all required
+external libraries, which you can use as:
+```
+conda env create -f environment.yaml
+```
+
+To enable GPU support for JAX, after the installation run:
+```
+pip install jaxlib==0.3.25+cuda${CUDA}.cudnn${CUDNN} -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+```
+
+For example, for CUDA 11.7, type:
+```
+pip install jaxlib==0.4.7+cuda11.cudnn86 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+```
+
+
+## Installation via PyPi
+
+Subsequently, install NicheCompass via pip:
+```
+pip install nichecompass
+```
+
+Install optional dependencies required for benchmarking, multimodal analysis, running tutorials etc. with:
+```
+pip install nichecompass[all]
+```
+
+[Mambaforge]: https://github.com/conda-forge/miniforge
+[Docker]: https://www.docker.com
+[PyTorch]: http://pytorch.org
+[PyTorch Scatter]: https://github.com/rusty1s/pytorch_scatter
+[PyTorch Sparse]: https://github.com/rusty1s/pytorch_sparse
+[bedtools]: https://bedtools.readthedocs.io