Here, we outline how to download and use the CLI on your own computer, and thus gain the capability to submit VCF files to the analysis pipeline via the command-line, bypassing unnecessary overhead through this website.

All our code can additonally be downloaded via the github repository: https://github.com/kauwelab/PolyRiskScore

Download the CLI scripts onto your computer

To get started, download these files onto your computer, which use a combination of Bash commands and Python scripts to call our server directly. Note: You must have Python 3 and Bash in the environment you plan to use the CLI.

Download CLI files

Unzip the zip file

The CLI scripts are compressed to allow for easy download. They must be unzipped in order to be used.

Using the Command-Line Interface

There are two ways the CLI tool can be used. First, you can run the Bash script without any parameters. This brings up the options of showing the usage statement or starting the interactive menu. Secondly, you can pass the correct parameters to the script and the calculator will automatically run.

Run Calculator From Interactive Menu

Run Calculator Directly From Command-Line