.emacs

(add-hook 'before-save-hook 'delete-trailing-whitespace)
;; use setq-default so modes that want tabs can enable this
(setq-default indent-tabs-mode nil)

(defun rick-sh-mode ()
  "2 space indent"
  (interactive)
  (setq sh-basic-offset 2
        sh-indentation 2))
(add-hook 'sh-mode-hook 'rick-sh-mode)

(defun rick-sh-mode-indent ()
  (setq sh-basic-offset 2
        sh-indentation 2)
  (indent-region (point-min) (point-max) nil)
  (save-buffer)
)

shell

rick@tao:~$ emacs -batch tmp.sh -l ~/.emacs -f rick-sh-mode-indent

# works