I wouldn't advise cloning a live system, but if you have enough space on the SD that you're running the Pi on, you could put the OS image on it, and expand it onto the new (USB connected) SD card, using the official install instructions.
It may take quite a while, but it does work.
Essentially, you'd put the new image file onto your existing Pi's SD card, plug in your USB SD card reader, figure out what the new drive is called, and:
sudo dd if=/path/to/image.img of=/dev/usb_sd bs=4M
Just be very careful you have the drives the right way around... the OS won't warn you if you try to overwrite your main SD card.