Installation

1. Prepare Python environment

To install PROST, we recommend using the Anaconda or Miniconda Python Distribution and creating an isolated environment, so that the PROST 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 PROST-master.zip file from github Code and unzip it.

git clone https://github.com/Tang-Lab-super/PROST.git

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

cd PROST-master

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

conda create -n PROST_ENV python=3.7
conda activate PROST_ENV

2. Prepare R environment

The PROST 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 PROST_ENV environment by:

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

3. Install dependency packages

a. If you want to install PROST in Linux environment, you can install the dependency packages using pip by:

pip install -r requirements.txt

b. If you want to install PROST in Windows environment, you can install the dependency packages using pip by:

pip install -r requirements_win.txt
pip install rpy2-2.9.5-cp37-cp37m-win_amd64.whl

4. Install PROST

Install the PROST package under PROST_ENVenvironment 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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