I'm deploying Jasper Reports Library on a Bitnamy EC2 instance on AWS with Tomcat installed; as I will use php pages in conjunctions with Jasperreports I'm deploying PHPJava/Bridge on Tomcat, but I'm not sure which permission must be set for jar files (for ex jasperreports-6.2.0.jar) in tomcat\webapps\JavaBridgePHP\WEB-INF\lib.
You question is not about JasperReports itself but about setting up PHP Java/Bridge. You'll probably get a better answer if you port your question to PHP Java/Bridge forum instead of here.
I'm not sure what you mean by "permission" because JasperReports library doesn't have any permission in itself. If you mean file system permission on linux instance, jar files require "r" privilege.