How to copy a directory which root can't access to a directory that only root can access?

You can use tar as a buffer process

cd .rubies
tar cf - ruby-2.1.3 | ( cd /opt && sudo tar xvfp - )

The first tar runs as you and so can read your home directory; the second tar runs under sudo and so can write to /opt.

You could use rsync or scp to copy from user@localhost to the local directory.

Example for rsync:

# rsync "$real_user@localhost:$PWD/.rubies/ruby-2.1.3" /opt

You could alternatively

$ rsync .rubies/ruby-2.1.3 "root@localhost:/opt"

if you let root access localhost directly (not recommended; we normally prefer root access to be via sudo).

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