Installation

This tutorial demonstrates how to install Pysodb on a method which use for spatial spot deconvolution.

Using tangram as an example, install Pysodb in its installation environment.

Reference tutorials presents can be found at https://github.com/broadinstitute/Tangram and https://github.com/TencentAILabHealthcare/pysodb.

Installing softwares and tools

1. The first step is to install Visual Studio Code, Conda, Jupyter notebook and CUDA in advance.

Reference tutorials presents how to install Reference tutorials presents how to install Visual Studio Code, Conda and Jupyter notebook, respectively. And they can be found at https://code.visualstudio.com/Docs/setup/setup-overview, https://code.visualstudio.com/docs/python/environments#_activating-an-environment-in-the-terminal and https://code.visualstudio.com/docs/datascience/data-science-tutorial., respectively.

2. Launch Visual Studio Code and open a terminal window.

Henceforth, various packages or modules will be installed via the command line

Installation Tangram

3. Select the installation path and open it

cd <path>

4. Create a conda environment

conda create -n <environment_name> python=3.8

5. Activate a conda environment

Run the following command on the terminal to activate the conda environment:

conda activate <environment_name>

6. Install Tangram package

pip install tangram-sc

7. Install squidpy package

pip install squidpy

Installation Pysodb

Keep the conda environment active

8. Clone Pysodb code

git clone https://github.com/TencentAILabHealthcare/pysodb.git

If cloning the code fails through git, please download it at https://github.com/TencentAILabHealthcare/pysodb, upload it to the folder created above, and extract it.

9. Open the Pysodb directory

cd pysodb

10. Install a Pysodb package from source code

python setup.py install

If “error: urllib3 2.0.0a3 is installed but urllib3<1.27,>=1.21.1 is required by {‘requests’}” appears, users can execute the following commands,respectively.

pip install 'urllib3>=1.21.1,<1.27'
python setup.py install

print('finish！')

finish！