The command to add a primary key in a migration is:
add_column :my_table, :id, :primary_key
However, the wording of your question suggests that your table already has an auto-increment column. Unless I’m mistaken, there are several DBMS that do not allow more than one auto-increment column on a table.
If you DO already have an auto-increment column and you actually want to use that column as your primary key, just add the following to your model:
set_primary_key "my_existing_column"
Or in more recent versions of Rails:
self.primary_key = "my_existing_column"
In the case that you already have an auto-increment column and you can’t use that as the primary key, you may be out of luck.