So I don't forget, the instructions to digitally sign a PDF in Linux are as follows:

First create a key using Java's keytool if you don't already have one. The command is

keytool -genkey -keyalg RSA -keysize 4096 -alias alias -keystore .keystore

Then, use JSignPDF to sign the PDF file. Make sure to select "JKS" from the keystore type.