I like to use htmlize-file in emacs to turn clojure source files into html.
I want to use it from the linux command line instead, or programmatically from clojure itself
The following Elisp code tells Htmlize to emit CSS class names instead of raw styles.
(setq org-export-htmlize-output-type 'css)
Then you can add CSS to your HTML file to get whatever colors you want. This works with Emacs in batch mode.