\documentclass{article}
\begin{document}
Including a LilyPond file with options (quote and noindent):

\lilypondfile[quote,noindent]{include2.ly}

From a subdirectory:

\lilypondfile[quote,noindent]{include/example.ly}

Within a lilypond block:

\begin{lilypond}[quote,noindent]
  \include "include/myvar.ily"
  \relative c'' { \myVar }
\end{lilypond}
\end{document}