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
I can't give you an ideal answer yet (I'm going to go do some research on this), but I have read that when invoked in batch mode, Emacs ignores display-specific commands like font-lock coloring. This makes execution of any script that uses display properties (like htmlize) problematic from batch mode.
I'm actually fairly interested in modifying htmlize at some point to allow color themes to be passed to it rather than using the current theme; what looks good in my Emacs session won't necessarily look good exported to HTML. For example, I tend to use blipp-blopp for htmlize, but I use midnight, comidia or charcoal while coding. I'm speculating that if htmlize could accept a color-theme specification directly, it might be able to avoid examining current font-lock properties and would then work from batch mode.
Sorry I couldn't be more helpful.