How do I run bibtex after using the -output-directory flag with pdflatex, when files are included from subdirectories?

Question

When I have master pdflatex file which includes one or more child documents using something like \include{include/childdoc}, and I call pdflatex on it using pdflatex -output-directory=out parent.tex, I seem unable to find a way of calling bibtex on the resulting parent.aux file. I have tried both cd out; bibtex parent, and bibtex out/parent, to no avail.

I know there are various build-tools out there, but I'd like first to make it work just from the shell with no special build-tool dependencies.

Answer 1

Ok I finally figured it out (not sure if this is documented somewhere already):

I needed to explicitly create directories within out having the same name as the directories I include files from. Then, I need to be in the out directory when running bibtex. Furthermore, the bibtex file needs to be manually copied to the out directory. Finally, I run pdflatex a second time from the top-level directory, again with the -output-directory flag.

In summary (starting in the directory containing parent.tex):

1. mkdir out/include
2. pdflatex -output-directory=out parent.tex
3. cp mybib.bib out
4. cd out ; bibtex parent
5. cd .. ; pdflatex -output-directory=out parent.tex

(and maybe you need to run pdflatex again, depending on what packages you're using...)

Answer 2

Did you check the location of the aux-files? The --output-directory doesn't affect auxiliary files (at least not in miktex. In miktex there is the --aux-directory switch to set the directory for auxiliary files). Also - as you use \include: Don't forget that they will be more than one aux-file.