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I am using Eclipse 4.2 with TeXlipse 1.5 (the version bundled with StatET 3.2) and MixTeX 2.9. I have no problem using TeXlipse, bibtex, and natbib to produce bibliographies. But I often want to include multiple bibliographies (i.e., lists of references) in the same document. natbib isn't up to this task. In these cases, I turn to the bibunits package.

The problem is that Texlipse doesn't work well with bibunits. When latex (or pdflatex, etc.) is run on a document that includes \usepackage{bibunits}, it generates an .aux file for each bibliography that is to be created: bu1.aux, bu2.aux, and so on. If the bibliographies are to be produced, bibtex needs to process each of these .aux files:

bibtex bu1.aux
bibtex bu2.aux

and so on. But Texlipse doesn't seem to know this. So it doesn't, by default, direct bibtex to process those .aux files. The result is that the bibliographies don't display as they should.

Here is a complete example of a document that the command-line tools (pdflatex, bibtex) handle fine but that gives Texlipse a lot of trouble. Although it uses bibunits, it has only one bibliography (to keep things simple):

\documentclass{article}
\usepackage{bibunits}
  \defaultbibliography{references}
  \defaultbibliographystyle{plainnat}
\usepackage{natbib}
\begin{document}
  \begin{bibunit}
    Lorem ipsum dolor \citep{Smith_Lorem_1980}.
    \putbib
  \end{bibunit}
\end{document}

where references.bib is

@BOOK{Smith_Lorem_1980,
  AUTHOR    = {John Smith},
  TITLE     = {Sit Amet},
  YEAR      = {1980},
  PUBLISHER = {Knopf},
}

(The example requires a separate .bib file: TeXlipse doesn't support \thebibliography commands.)

Is there a way to change the Texlipse configuration so that it can handle the .aux file that is generated when files like the example file are processed? Right now, I have rigged up a workaround (configuring BibTeX as an "external tool" to process the .aux files), but it is clunky.

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You can setup your editor for arara to simplify the compilation. –  Marco Daniel May 26 '13 at 11:59
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