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.