In
debian stable (and probably the others) , there is an iptables startup script
which is quite nice.
Put
your rules into /var/lib/iptables/active in the format as saved by
iptables-save
Also,
put in a ruleset in /var/lib/iptables/inactive for the rules that should exist
when you stop the firewall.
They
use /etc/init.d/iptables to start, stop, etc. You can also load and save
other sets of rules, but the default ones it uses are active and inactive.
To get it to start on startup use update-rc.d - as far as I
remember something "update-rc.d iptables defaults" will do
it.
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