Does $fooDir contain spaces? Why are you adding the extra quotes around the command name?

You really should be checking the return value of system: system(...) == 0 or die "system failed, \$?=$?"; (see the docs for more detailed error checking).

Also, I'm sure you know you really should be using strict.

You probably should look into some modules such as IPC::Run3 or IPC::System::Simple for easier and "safer" execution of external commands.

Lastly, you can look into modules such as File::Spec, File::Path and friends for better handling of filenames and file operations.