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Are there any packages which depend on other 'non-standard' command line programs (i.e. not pdflatex, bibtex and friends)?

When writing a document in e.g. LaTeX, this of course needs to be compiled with e.g. pdflatex. With a bibliography, this requires a separate call to bibtex (or biber), another command-line program.

I have found that makeglossaries and makeindex are two such commands (used by the packages glossaries and makeidx, respectively). Are there any more which are in common use, perhaps with their own associated auxillary files?

I'm asking as I'm trying to automate the compiling process a little for common-use cases. While `latexmk' is great, it doesn't appear to support glossaries at this time.

Updated - sorry latexmk can be tweaked to include makeglossaries as below, afraid I didn't know about this.

Updated - there are indeed a lot of these 'supporting' commands. @Nicola Talbot's comment gives the longest list (http://ctan.org/tex-archive/support) - again, new to me and will be glad to accept as an answer. Agreed that makeindex is now standard; by 'common-use' I guess it's my own use case. ChkTeX looks like integrating into the workflow. try also looks like a good approach to integrating these command-line steps.

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    latexmk does support glossaries; see tex.stackexchange.com/questions/1226/…
    – lockstep
    Mar 15, 2015 at 15:54
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    makeglossaries invokes either makeindex or xindy, according to requirements, but I wouldn't call makeindex any more "non-standard" than bibtex as both have been available with TeX distributions for a long time.
    – Nicola Talbot
    Mar 15, 2015 at 16:09
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    There will be lots. What do you count as 'common-use'? graphicx/graphics/standalone/tikz/etc. can use convert (and similar). tikz/pgf/pgfplots can use gnuplot. python, sage, asymptote. I guess that metapost must surely count as standard but what about the auxiliary wrappers for conversion to PDF? Also, there are variants of bibtex such as bibtex8.
    – cfr
    Mar 15, 2015 at 16:17
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    There are several sub-directories on CTAN that list applications, such as tex-archive/indexing, tex-archive/biblio and tex-archive/support
    – Nicola Talbot
    Mar 15, 2015 at 16:19
  • pythontex comes to mind.
    – egreg
    Mar 15, 2015 at 17:09

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(Converting my comment into an answer.) There are a number of sub-directories on CTAN that list supporting applications. The main one is tex-archive/support, but there are also some subject specific sub-directories, such as tex-archive/indexing (indexing applications) and tex-archive/biblio (bibliographic applications). The tex-archive/graphics directory has a mixture of packages and applications.

I think the oldest supporting applications that are widely in use are probably makeindex, which was created by Pehong Chen in 1987, and bibtex, which was created by Oren Patashnik and Leslie Lamport in 1985. The 1985 version of "LaTeX: A Document Preparation System" mentions bibtex. It doesn't mention makeindex but does document the commands \makeindex, index, \makeglossaries and \glossaries that are used to create external files that can be post-processed by LaTeX.

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