If the citation is in the glossary, it won't be picked up until the glossary exists. So you first need to run (pdf)latex, then run makeglossaries to generate the glossary file, then run (pdf)latex which will display the glossary so the citation can now be picked up by LaTeX, then run bibtex to generate the bibliography file, then run (pdf)latex twice to ensure the citations are up-to-date.
% arara: pdflatex
% arara: makeglossaries
% arara: pdflatex
% arara: bibtex
% arara: pdflatex
% arara: pdflatex
\documentclass{article}
\usepackage{glossaries}
\begin{filecontents}{test.bib}
@article{Sample,
title = "Sample title",
author = "Sample Author",
journal = "Sample Journal",
year = 2013
}
\end{filecontents}
\makeglossaries
\newglossaryentry{sample}{name=sample,description={an example with a
citation~\cite{Sample}}}
\begin{document}
\gls{sample}.
\printglossaries
\bibliographystyle{plain}
\bibliography{test}
\end{document}