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Makefile
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Makefile
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DATA=
FIGURES=
# To add a new illustration, add a line for the corresponding figure name
# here (use hyphens to separate words, not underscores). Then, define
# the corresponding function/command in illustrations.py, making
# sure that it writes out the corresponding SVG file. The Makefile will
# take care of the rest.
# NB: ensure that any additional static files that must be stored in
# git are put in the illustrations/assets directory.
ILLUSTRATIONS=\
illustrations/ancestry-resolution.pdf \
illustrations/simplification.pdf \
illustrations/arg-in-pedigree.pdf \
illustrations/inference.pdf \
illustrations/cell-lines.pdf \
illustrations/simplification-with-edges.pdf \
all: paper.pdf response-to-reviewers.pdf response-to-reviewers-2.pdf
paper.pdf: paper.tex paper.bib ${DATA} ${FIGURES} ${ILLUSTRATIONS}
pdflatex -shell-escape paper.tex
bibtex paper
pdflatex paper.tex
pdflatex paper.tex
inference_inputs: \
examples/Kreitman_SNP.samples \
examples/Kreitman_SNP.matrix \
examples/Kreitman_SNP.sites \
examples/Kreitman_SNP.haps \
inference_outputs: \
inference_inputs \
examples/Kreitman_SNP_tsinfer.trees \
examples/Kreitman_SNP_kwarg.trees \
examples/Kreitman_SNP_argweaver.trees \
examples/Kreitman_SNP_relate_merged.trees \
examples/Kreitman_SNP.samples: make_example_inputs.py
python make_example_inputs.py tsinfer-input
examples/Kreitman_SNP.matrix: make_example_inputs.py
python make_example_inputs.py kwarg-input
examples/Kreitman_SNP.sites: make_example_inputs.py
python make_example_inputs.py argweaver-input
examples/Kreitman_SNP.haps: make_example_inputs.py
python make_example_inputs.py relate-input
examples/Kreitman_SNP_tsinfer.trees: make_example_outputs.py
python make_example_outputs.py run-tsinfer
examples/Kreitman_SNP_kwarg.trees: make_example_outputs.py
python make_example_outputs.py run-kwarg
examples/Kreitman_SNP_argweaver.trees: make_example_outputs.py
python make_example_outputs.py run-argweaver
examples/Kreitman_SNP_relate_merged.trees: make_example_outputs.py
python make_example_outputs.py run-relate
illustrations/%.svg: illustrations.py
python illustrations.py $*
%.pdf : %.svg
# Needs inkscape >= 1.0
inkscape --export-type="pdf" $<
paper.ps: paper.dvi
dvips paper
paper.dvi: paper.tex paper.bib
latex paper.tex
bibtex paper
latex paper.tex
latex paper.tex
.PHONY: spellcheck
spellcheck: aspell.conf
aspell --conf ./aspell.conf --check paper.tex
clean:
rm -f *.pdf
rm -f *.log *.dvi *.aux
rm -f *.blg *.bbl
mrproper: clean
rm -f illustrations/*.pdf
rm -f illustrations/*.svg
rm -f *.ps *.pdf
review-diff.tex: paper.tex
latexdiff reviewed-paper.tex paper.tex > review-diff.tex
review-diff.pdf: review-diff.tex
pdflatex review-diff.tex
pdflatex review-diff.tex
bibtex review-diff
pdflatex review-diff.tex
response-to-reviewers.pdf: response-to-reviewers.tex
pdflatex $<
review-diff-2.tex: paper.tex
latexdiff reviewed-paper-2.tex paper.tex > review-diff-2.tex
review-diff-2.pdf: review-diff-2.tex
pdflatex review-diff-2.tex
pdflatex review-diff-2.tex
bibtex review-diff-2
pdflatex review-diff-2.tex
response-to-reviewers-2.pdf: response-to-reviewers-2.tex
pdflatex $<