no, unless the tools are used as a library in a web server.

It's worth noting picard.jar and abra.jar are affected (even though as Pierre L says, these are unlikely to be attacked on most systems).

If you're responsible for systems, esp web servers, it would pay to upgrade by downloading the latest jar and removing the older ones.

Not sure how bad a problem this could be with Galaxy webservers for example, where picard is used widely.