Do not want to allow Queries to take more than x minutes? Do not want to allow Queries to take more than x minutes ! What System variable can I set to automatically terminate it.
In mysql 5.7 ; you can use max_execution_time
From the documentation:

Statement Execution Time Optimizer Hints
The MAX_EXECUTION_TIME hint is permitted only for SELECT statements. It places a limit N (a timeout value in milliseconds) on how long a statement is permitted to execute before the server terminates it:
MAX_EXECUTION_TIME(N)

Example with a timeout of 1 second (1000 milliseconds):
SELECT /*+ MAX_EXECUTION_TIME(1000) */ * FROM t1 INNER JOIN t2 WHERE ...

The MAX_EXECUTION_TIME(N) hint sets a statement execution timeout of N milliseconds. If this option is absent or N is 0, the statement timeout established by the max_execution_time system variable applies.
The MAX_EXECUTION_TIME hint is applicable as follows:

For statements with multiple SELECT keywords, such as unions or statements with subqueries, MAX_EXECUTION_TIME applies to the entire statement and must appear after the first SELECT.

It applies to read-only SELECT statements. Statements that are not read only are those that invoke a stored function that modifies data as a side effect.

It does not apply to SELECT statements in stored programs and is ignored.