The x, y and z parameters to glRotate can specify any arbitrary axis, not just the x, y and z axes. To find an axis passing through your line, just subtract the end-points of the line to get an axis vector: if the two points are (x1, y1, z1) and (x2, y2, z2) the axis you need is (x2-x1, y2-y1, z2-z1) .
I've done that using small "patch" on my Vector class.
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