Hi Bika:

The exception in your catalina.out file shows what's happening:
Caused by: java.lang.IllegalArgumentException: The main resource set specified [/usr/local/labkey/apps/apache-tomcat-9.0.82/webapps/labkey] is not a directory or war file, or is not readable (it does not exist or permissions to access it are missing)

This indicates that it's 'looking for' LabKey under your tomcat installation instead of under the LabKey enlistment where it almost certainly is located. We use $LABKEY_HOME as shorthand in our docs for the variable location of that installation. However, the way you have this in your labkey.xml file:
docBase="LABKEY_HOME/labkeywebapp"

...it's trying to find a relative path under tomcat, i.e. a directory with that variable name, which isn't right. Replace LABKEY_HOME in your labkey.xml file with the absolute path to where it is instead. For example, something like this if you followed our installation docs:
docBase="/usr/local/labkey/labkey/labkeywebapp"

Hope that helps,
--Molly