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1) Login to your box as root
2) Download the APF Source (current version 0.9.3.3)

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# wget http://www.rfxnetworks.com/downloads/apf-current.tar.gz

3) Extract the tar.gz

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# tar -zxf apf-current.tar.gz

4) Enter the APF directory

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# cd apf-0.9.3_3

5) Run install code

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./install.sh

6) Modify the APF config File

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#vi /etc/apf/conf.apf

Hit i to enter insert mod
7) Add in the ports you want to open for inbound (INGRES). The following is for a cPanel box

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# Common ingress (inbound) TCP ports

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IG_TCP_CPORTS=" 20,21,22,25,26,53,80,110,143,443,465,993,995,2082,
2083,2086,2087,2095,2096,3306,6666"

# Common ingress (inbound) UDP ports

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IG_UDP_CPORTS="21,53,465,873"

# Common ICMP (inbound) types
# 'internals/icmp.types' for type definition; 'all' is wildcard for any
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G_ICMP_TYPES="3,5,11,0,30,8"


Please note that the above variables are already there, I placed what should be in there

8) Tell APF to monitor out going (EGRESS) also

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Change the line:
EGF="0"
to
EGF="1"

9) Tell APF what ports to monitor

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# Common egress (outbound) TCP ports

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EG_TCP_CPORTS="21,22,25,26,37,43,53,80,110,113,443,465,873,2089,3306"

# Common egress (outbound) UDP ports

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EG_UDP_CPORTS="20,21,53,465,873"

# Common ICMP (outbound) types
# 'internals/icmp.types' for type definition; 'all' is wildcard for any

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EG_ICMP_TYPES="all"

10) Save and exit - hit 'esc' :wq 'enter'

11) Start APF

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# /usr/local/sbin/apf -s

You may or may not get output, if you do please reply and I can advide as to what to fix. If all goes well ou go back to the command line.
You now want to verify everything works, you can still get into SSH, cPanel works, you can view a page, etc.

12) If all works edit the config file and change the developer mode to 0

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# vi /etc/apf/conf.apf

Hit i to enter insert mode

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Change
DEVM="1"
to
DEVM="0"


Save and quit
Hit 'esc' :wq 'enter'

13) Restart APF


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# /usr/local/sbin/apf -r

APF is now installed and monitoring your server.