Not an easy task. Just about any adhesive may be visible. If the surface of the wood is flat, a very thin coating of GE Silicone II spread so there is no voids will provide good adhesion, and any squeeze out can be razor bladed off when dry. The silicone may not dry completely clear. Other than CA glue (which may not give enough time), getting the glued surface to be completely clear of voids (dry spots), may be very difficult. What is the application?
I am a little puzzled as to what you are building. Are you applying wood trim to the suface of a clear glass door, or are you surrounding glass with wood trim? Clear silicone, as suggested by Cabinetman would probably be the best bet if you are applying the wood directly to the surface of the glass. If however, you are wanting to suround a piece of glass with wood trim, the the best idea would be to rabbet a groove in the trim so the glass fits into it.
Perhaps you can give us a better idea of what you are making, and we could be of more help.
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