so i am writing this little how to just incase you are also having this problem.
if you are getting this error: cp: omitting directory
this is what you need to do:
cp -r orginal_file new_file
so the trick here is to add the -r escape on your command and it shouldn't give you an error anymore
the -r options if for recursive, meaning copy all the files within a directory. the mostly likely reason you are getting this error is because you are trying to copy a directory which has other files or other sub-directories, so you need to tell linux to copy all the files withing (recursive).
hope this helps.
if you ever need web hosting, visit www.webune.com they have excellent service.