When you say, you downloaded code from GitHub, I guess you cloned https://github.com/wso2/platform
WSO2 currently uses SVN as the main source repository and therefore I recommend you to use the SVN repository. Following has the current WSO2 Carbon code.
https://svn.wso2.org/repos/wso2/carbon/
Before checking out the code, please make sure you understand how the SVN repository is structured.
There are many resources on the web about building WSO2 Carbon from source. Please search on the web. Here is my answer given to a similar question about building from source.
FYI: WSO2 just released Carbon 4.2.0 and therefore we currently use the 4.2.0 branches.