EHR-QC-Standardise¶
Follow the below steps to install EHR-QC-Standardise in your computer.
Login¶
Upon login to a system and opening a terminal, the following prompt should appear, where the user is the user name and the hostname is the hostname of the system.
user@hostname:~$
Change directory¶
From the home directory which will be open by default, change to a suitable directory on your computer where the utility needs to be installed. For example, in this tutorial we have changed to workspace directory.
user@hostname:~$ cd workspace
Clone¶
In the destination folder, clone the current version of EHR-QC repository from the GitHub.
user@hostname:~/workspace$ git clone <Add GitLab repo link here>
Open EHR-QC¶
Open the EHR-QC-Standardise directory that is downloaded from GitHub after cloning.
user@hostname:~/workspace$ cd EHR-QC-Standardise
Python virtual environment¶
The Python virtual environment encaptulates all the libraries required for the EHR-QC-Standardise. All the necessary libraries listed in a requirements.txt file that can be found at the root of the repository. Below are the instructions to create and install dependancies in the Python virtual environment.
Note
EHR-QC-Standardise requires Python version 3.9 or higher. For installing Python, please refer the below link: https://www.python.org/downloads/
Create virtual environment¶
Inside the EHR-QC-Standardise directory, create a new Python virtual enviroment to conveniently manage all the dependencies required for the utility.
user@hostname:~/workspace/EHR-QC-Standardise$ python3 -m venv .venv
Activate virtual environment¶
After creating the Python virtual enviroment, activate the virtual enviroment to start using it for subsequent commands. The prompt will change with (.venv) appearing in front of it as shown below;
user@hostname:~/workspace/EHR-QC-Standardise$ source .venv/bin/activate
(.venv) user@hostname:~/workspace/EHR-QC-Standardise$
Install dependencies¶
Install all the required dependencies listed in the requirements.txt file in the newly created Python virtual environment.
(.venv) user@hostname:~/workspace/EHR-QC-Standardise$ pip install -r requirements.txt
Verify¶
Verify the installation by running the following command. The expected output should contain EHR-QC <version number>.
(.venv) user@hostname:~/workspace/EHR-QC-Standardise$ python -m EHR-QC -v
EHR-QC 1.0