Instrument transposition and score transposition confusion

[OnionRingOfDoom]

I'm writing an orchestral score out, and I have a large piece.ly file in
which all the individual instrument parts music is written out. Every
instrument's part starts with something like varInstrumentNotes = \relative
c'' { . Every part is entered with \relative c, then there are template
files for each part which are used to actually print the invidual parts. The
structure is as follows:

\new Staff \with {

} % end with
{
  \clef "treble"
  \set Score.skipBars = ##t
  \override MultiMeasureRest #'expand-limit = 1
  \override Score.RehearsalMark #'Y-offset = #0.08
  \varKey
  \varTime
  \varInstrumentNotes
}

But now I have to write out the Bb Clarinet parts, and the Bb Clarinet is
obviously in the key of Bb. Now, in the score, I want to write it out in C,
and then in the template file have it transpose to Bb. The key of the entire
piece is A Minor. How would I go about transposing the Bb Clarinet into the
propper key? I cannot seem to figure out if I use the \transpose command or
the \transposition command.
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