Installation

This tutorial demonstrates how to install Pysodb on a method which use for alignment.

Taking paste as an example, install Pysodb in its installation environment.

Reference tutorials presents can be found at https://github.com/raphael-group/paste and https://github.com/TencentAILabHealthcare/pysodb.

Installing softwares and tools

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

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.

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

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

Installation PASTE

3. Select the installation path and open it

[ ]:

cd <path>

4. Clone PASTE code

[ ]:

git clone https://github.com/raphael-group/paste.git

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

5. Open the PASTE directory

[ ]:

cd paste

6. Create a conda environment

[ ]:

conda create -n <environment_name> python=3.8

7. Activate a conda environment

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

[ ]:

conda activate <environment_name>

8. Install paste package

[ ]:

pip install paste-bio

9. Install other packages required for paste

[ ]:

pip install -r requirements.txt

Pysodb installation

Keep the conda environment active

10. 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.

11. Open the Pysodb directory

[ ]:

cd pysodb

12. 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

[1]:

print('finish！')

finish！