open my $pipe,'run.bat |' or die "Ooops: $!";
while (my $line=<$pipe>) {
    print $line; # <-- stupid example
}
close $pipe;

##</code><code>##

open my $pipe,'run.bat 2>&1 |' or die "Ooops: $!"; 
# ...

##</code><code>##

open my $pipe,'run.bat 2>&1 >nul |' or die "Ooops: $!"; 
# ...

##</code><code>##

open my $pipe,'java.exe -jar jarfile.jar arg1 arg2 |' or die "Ooops: $!";
# ...