From your IDE, create a remote debug configuration, configure it for the default JPDA Tomcat port which is port 8000.
From the command line:
Linux:
cd apache-tomcat/bin
export JPDA_SUSPEND=y
./catalina.sh jpda run
Windows:
cd apache-tomcat\bin
set JPDA_SUSPEND=y
catalina.bat jpda run
Execute the remote debug configuration from your IDE, and Tomcat will start running and you are now able to set breakpoints in the IDE.
Note:
The JPDA_SUSPEND=y line is optional, it is useful if you want that Apache Tomcat doesn't start its execution until step 3 is completed, useful if you want to troubleshoot application initialization issues.