Installation

1. Prepare Python environment

To install SpaGT, we recommend using the [Anaconda](https://anaconda.org/) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html) Python Distribution and creating an isolated environment, so that the SpaGT and dependencies don’t conflict or interfere with other packages or applications. Please install the conda in advance.

Create environment First, please download or clone the SpaGT.zip file from github Code and unzip it.

git clone https://github.com/xy428/SpaGT.git

The entire installation process takes place in the SpaGT directory, so first go to that directory by:

cd SpaGT

We recommend using a conda environment to configure SpaGT. To create and activate the environment SpaGT_ENV, run the following command in bash or Anaconda Powershell Prompt:

conda create -n SpaGT_ENV python=3.8
conda activate SpaGT_ENV

2. Prepare R environment

The SpaGT uses the mclust package in the R language environment, and links it in a Python environment via rpy2. You can install the R language environment under SpaGT_ENV environment by:

conda install -c conda-forge r-base
conda install -c conda-forge r-mclust=5.4.10

3. Install dependency packages

If you want to install SpaGT, you can install the dependency packages using pip by:

pip install -r requirements.txt

4. Install SpaGT

Install the SpaGT package under `SpaGT_ENV`environment by:

pip install setuptools==58.2.0
python setup.py build
python setup.py install

Here, the environment configuration is completed!

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