This blog post is quite easy, it shows you how to install rkhunter on a linux machine and how to configure rkhunter to run periodically using a cron job.
RKhunter (rootkit hunter) is a program that takes a fingerprint of installed files and directories in your machine during install and compares the stored fingerprint against a fingerprint taken later on. It uses this fingerprint to determine if the files have changed, or if any files have been added or altered.

Install rkhunter on a linux machine

Login to your server (via SSH and su to root)

cd /usr/local/src/

Go here and find the latest version.. Right now the latest version is 1.4.2

Download RKHunter

wget http://downloads.sourceforge.net/project/rkhunter/rkhunter/1.4.2/rkhunter-1.4.2.tar.gz?r=&ts=1437775186&use_mirror=netcologne

Extract files

tar -xzvf rkhunter*
cd rkhunter*
./installer.sh --install

Thats the section on how to install rkhunter done, next on to some things that will help you using rkhunter.

daily reports using a cronjob

setup RKHunter to e-mail you you daily scan reports.

vi /etc/cron.daily/rkhunter.sh

Add The Following:

#!/bin/bash
/usr/local/bin/rkhunter -c --cronjob 2>&1 | mail -s "RKhunter Scan Details" replace-this@with-your-email.com

Replace the e-mail above with your e-mail!! It is best to send the e-mail to an e-mail off-site so that if the box IS compromised the hacker can’t erase the scan report unless he hacks another server too.

chmod +x /etc/cron.daily/rkhunter.sh

next, update rkhunter so that all the components are the latest versions

rkhunter --update

Then you can run a scan against your system

rkhunter -c --sk --display-logfile 

Once the scan completes you can go through the list produced and fix the various things!