Assumed, your SuisseID Smartcard already is working on your Linux workstation.

1. Download LocalSigner from Open eGov Plattform of Confoederatio Helvetica
2. Untar it to ~/opt or wherever you want

   tar xvzf localsigner_4.1.3_linux.tar.gz --directory=~/opt

3. Make sure you use Java 8 (Oracle or OpenJDK). I had some issues with openJDK 10
4. run localsigner

   ~/opt/LocalSigner/local-signer.sh

5. If the PDF is not PDF/A, then a "convert" button is shown, hit it
6. the rest is self-explanatory, select a source and a destination, then click on "sign" on the bottom-right
7. to check the signature, there is a command line tool. Run:

   pdfsig ~/path/signed-file.pdf