There should (already) be policy modules for each of these applications. If they are not installed / enabled by default you may need to do so manually.
This link discusses policy modules and how to enable and disable them. I would start here and then look for these modules and see if they are enabled. link1:
Second, this document goes into a lot of detail regarding troubleshooting with SELinux. While starting out, set your mode to permissive which will still cause exceptions to be logged but won't interfere with operations. You can then evaluate the AVC messages and even use the tool audit2allow to help evaluate a course of action.
Third, the gentoo documentation on SELinux is pretty good, including a discussion of roles, contexts, and what not. If you find that you are having problems, most likely it is going to be because your missing a component.
Actually I want to know which SELinux rules should I set when I ran apache, nagios and Squid?
I always disabled SELinux when I ran apache, nagios and squid.
Thanks for your SELinux link.
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