[Tex/LaTex] bibtex aux-files directory

auxiliary-filesbiberbibtexmiktexoutput

Preamble: Setting the output directories

TeX distros have the useful command line option --output-directory to create all output files in a specified directory.

MikTeX provides an even more convenient option to put only temporary material in a separate folder, which can be eventually deleted, that is:

pdflatex --aux-directory=auxdir mybook

--aux-directory is particularly convenient for large projects with several TeX files, for example a book with several chapters, to reduce post-compilation clutter.

One can use together --aux-directory and --output-directory.
Below I will address --aux-directory, but using --output-directory or both produces the same issue.

Using bibliographies when output/aux directories are diverted

I haven't yet tried them, but I am aware of --input-directory and --output_directory option, which should do similar jobs in biber.

As regards BibTeX, there are no such options. For a simple project, based on a single .tex file (and therefore .aux), depending on your path separator,

bibtex auxdir/mybook 
bibtex auxdir\mybook

should work. If there are several .tex files (when the aux dir is actually useful), bibtex is unable to find the other aux files, which will still be searched in the project's root dir.

It is possible to cd to auxdir, but in this case the .bib and .bst files will not be found.
A workaround consists in copying them in the auxdir. That works, but it is against the purpose of such directory and also time-consuming, as the original .bib file in the parent directory is likely to be updated often.

What is the correct workflow for bibtex and biber when the --aux-directory (--output-directory) option is employed?

Best Answer

So some suggestions:

1. Don't use --output-directory or --aux-directory

Really. They just add a whole layer of unnecessary complexity. In addition to issues with bibtex, if you have use multiple input files, you'll likely end up having to recreate the same folder hierarchy in the output directory as you have in the main directory. Especially for large, multi-part documents, this can be a hassle for no real added value. Similarly, if you use other external tools, you'll end up needing to configure them to use the output directory appropriately.

2. Use latexmk

This will handle bibtex in an appropriate way and handle the issue with the output hierarchy detailed above. This is probably the simplest way to deal with things, if you insist on using an output directory.

3. A way to make things work

If you still want to use an output directory and don't want to use latexmk, you can do the same thing that latexmk does. From the command prompt, you can run bibtex like this (all one line):

cd auxdir & set BIBINPUTS="C:\path\to\mybook;%BIBINPUTS%" & set BSTINPUTS="C:\path\to\mybook;%BSTINPUTS%" & bibtex mybook

Which runs bibtex in the auxdir, while adding the directory containing the source files to the bib / bst search path.

Related Solutions

[Tex/LaTex] How to use the Vim LaTeX-Suite multiple compile option with BibTeX and the -aux-directory option

There are several tools which can can help you.

arara

The cool tool arara provides several rules to specify all compilation steps from inside the document.

For example you want to compile with pdflatex+bibtex+pdflatex you need the following lines in the preamble of the main document:

% arara: pdflatex
% arara: bibtex
% arara: pdflatex

After this specifications you can compile your document with

arara myfile.tex

Options to the rules can be given too.

% arara: pdflatex: { options: { -aux-directory=auxdir }  }
% arara: bibtex: { files: [auxdir/filename1, auxdir/filename2] }

TrY

Another but equal method is the tool TrY. It works only for Unix systems and instead of rules you can type complete small scripts.

The adapted example from above with TrY is:

%$ pdflatex myfile.tex
%$ bibtex myfile.aux
%$ pdflatex myfile.tex

and the compilation step is:

try myfile.tex

[Tex/LaTex] Placing Intermediate and Output Files in Another Folder

As suggested by lockstep, I write a short answer: AFAIK, this is currently not possible, because the path cannot be changed for the messages / log viewer and for the pdf viewer from within the Texmaker GUI. There is a feature request on the Texmaker issue list to make the path configurable: http://code.google.com/p/texmaker/issues/detail?id=97 Maybe you are lucky and in a later release this will be available. I personally would also use this new feature (and only backup the input folder, not the output folder).