Comment by graphene

I do something similar, here's my Makefile -- I have scripts that build figures in a separate directory, /figures. I'm sure it could be terser, but it does the job for me.

    texfiles = acronyms.tex analytical_mecs_procedure.tex analytical_mecs.tex \
               anderson_old.tex background.tex chaincap.tex \
               conclusions.tex cvici.tex gold_chain_test.tex introduction.tex \
               main.tex mcci_manual.tex methods.tex moljunc.tex \
               tb_sum_test.tex times_procedure.tex tm_mcci_workflow.tex tmo.tex \
               vici_intro.tex
 
    # dynamically generated figures
 
 
    all: main.pdf
 
    main.pdf: $(texfiles) figures/junction_occupations.pdf figures/overlaps_barplot.pdf \
                          figures/transmission_comparison.pdf \
                          figures/wigner_distributions.pdf
        pdflatex main.tex && bibtex main && pdflatex main.tex && pdflatex main.tex
 
    figures/junction_occupations.pdf: figures/junction_occupations.hs
        ghc --make figures/junction_occupations.hs
        figures/junction_occupations -w 800 -h 400 -o figures/junction_occupations.svg
        inkscape -D -A figures/junction_occupations.pdf figures/junction_occupations.svg 
 
    figures/overlaps_barplot.pdf: figures/overlaps_barplot.py
        python figures/overlaps_barplot.py
 
    figures/transmission_comparison.pdf: figures/transmission_comparison.py
        python figures/transmission_comparison.py
 
    figures/wigner_distributions.pdf: figures/wigner_distributions.py
        python figures/transmission_comparison.py
 
    clean:
        rm *.log *.aux *.blg *.bbl *.dvi main.pdf