The simplest way is to use in command line:
git difftool --tool=meld
or for merging:
git mergetool --tool=meld
where meld is a command for your application. In my case it is meld.
If you don't want every time specify it you have to configure globally:
git config --global diff.tool meld
git config --global merge.tool meld
Now it is possible to run them executing only
git difftool or
git mergetool in you repository directory.