Remove the window mulls---the trim around glass---carefully with a putty knife, small pry bar and a hammer and lay the to the side for installation. If there are any nails remaining in the trim, gently remove them. Always wear gloves to prevent injury from the glass. There is no need to remove the door for the replacement of the broken glass.
Remove the broken glass from the opening. Usually, tiny fragments of glass will remain stuck to the original caulk around the inside the window opening. Use the putty knife to scrape and clean any remaining glass from the surface.
Measure the empty opening, from left to right and from top to bottom. Take away 1/4 inch from both measurements. This will be the size of glass needed.
Lay out the piece of glass that you purchased. Make sure the surface is flat and large enough to handle the piece of glass. Make the desired marks with a permanent marker and place a straight edge against the marks. Gently scribe the glass cutter across the line. You will need to make several gentle passes and not one deep cut. A deep cut will cause the glass to break.
Apply small bead of clear silicone caulk around the perimeter of the glass opening. Gently press the piece of glass into the caulk. Place a small bead around the inside edges of the installed glass and replace the trim, one piece at a time, paying special attention to the way the trim came off. Using the same size nails, gently tap nails into the same holes.