You can enclose your shell command in backticks (``), or you can use the system command.

However, for portability it's generally best to try and avoid invoking the shell where-ever possible and either make use of perl inbuilt commands or modules.

For example, instead of using "cp", you could use File::Copy, you could use the builtin mkdir function, and for "scp" you could make use of Net::SCP

Cheers,
Darren :)