To run the lexer you need to have the following installed in cygwin (https://www.cygwin.com/):  
-Flex package (https://cygwin.com/cgi-bin2/package-grep.cgi?grep=flex&arch=x86_64)  
-Bison package (https://cygwin.com/cgi-bin2/package-grep.cgi?grep=bison&arch=x86_64)  
-gcc pacakge (https://cygwin.com/cgi-bin2/package-grep.cgi?grep=gcc&arch=x86_64)

After that you compile and run the lexer as following:  
flex lexer.l     // lexer.l is the lexer file  
gcc lex.yy.c  -o lexer -lfl    // where lex.yy.c is the result of "flex lexer.l"  
./lexer input_file             // lexer is the executable and we will set up main() to take in an input file  

As an input file you can use any of the examples in "Simple C Language"