You can use Wine to run Windows-only Application within Ubuntu.
Wine supports MetaTrader and you would be able to run it fine. However, you would have to use the Development Version of Wine as
MetaTrader4 requires Wine 1.5.4 and
MetaTrader5 requires Wine 1.5.9. Look at this link which gives further information about running MetaTrader under Wine. The latest Wine Development Release is 1.5.20 and you should install this version for greater compatibility.
Step 1 : Add Wine PPA to your software sources:
sudo add-apt-repository ppa:ubuntu-wine/ppa
Step 2 : Update your software sources:
sudo apt-get update
Step 3 : Install latest development release of Wine:
sudo apt-get install wine1.5
Step 4 : Run the executable Setup File
*.exe for your version of MetaTrader to install it as you normally do in Windows.