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Makefile
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FIGURES=figures/data-scaling.pdf\
figures/whole-matrix-compute.pdf\
figures/whole-matrix-compute-zarr-versions.pdf\
figures/whole-matrix-decode.pdf\
figures/subset-matrix-compute.pdf\
figures/subset-matrix-compute-supplemental.pdf\
figures/s3-throughput.pdf\
figures/s3-network-throughput.pdf \
figures/ofh-histograms.pdf
all: paper.pdf response-to-reviewers.pdf
paper.aux: paper.tex
pdflatex -shell-escape paper.tex
paper.bbl: paper.aux paper.bib
bibtex paper
pdflatex -shell-escape paper.tex
paper.pdf: $(FIGURES) paper.bbl
pdflatex -shell-escape paper.tex
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 *.log *.dvi *.aux
rm -f *.blg *.bbl
rm -fR _minted*
mrproper: clean
rm -f *.ps *.pdf
TS_FILES=scaling/data/chr21_10_1.ts\
scaling/data/chr21_10_2.ts\
scaling/data/chr21_10_3.ts\
scaling/data/chr21_10_4.ts\
scaling/data/chr21_10_5.ts\
scaling/data/chr21_10_6.ts
# Should probably add rules for other data collection. However, it
# takes a *long* time to do some stuff, and needs to be done in bits
# in practise.
plot_data/data-scaling.csv:
python3 src/collect_data.py file-size $(TS_FILES) -o $@
# Compression benchmarks:
plot_data/shuffle_benchmarks.csv:
python3 src/compression_benchmarks.py --input real_data/data/WGS/chr22.zarr \
--test-config shuffle \
-o $@
plot_data/compressor_benchmarks.csv:
python3 src/compression_benchmarks.py --input real_data/data/WGS/chr22.zarr \
--test-config compressor \
-o $@
plot_data/chunksize_benchmarks.csv:
python3 src/compression_benchmarks.py --input real_data/data/WGS/chr22.zarr \
--test-config chunksize \
-o $@
plot_data/chunksize_finegrained_benchmarks.csv:
python3 src/compression_benchmarks.py --input real_data/data/WGS/chr22.zarr \
--test-config chunksize_finegrained \
-o $@
# TODO make rule for time-scaling
# TODO make some substitution rules for this later
figures/data-scaling.pdf: plot_data/data-scaling.csv
python3 src/plot.py data-scaling plot_data/data-scaling.csv \
figures/data-scaling.pdf
figures/s3-throughput.pdf: plot_data/gel-s3-throughput.csv
python3 src/plot.py s3-throughput plot_data/gel-s3-throughput.csv \
figures/s3-throughput.pdf
figures/s3-network-throughput.pdf: plot_data/gel-s3-network-throughput.csv
python3 src/plot.py s3-network-throughput plot_data/gel-s3-network-throughput.csv \
figures/s3-network-throughput.pdf
figures/ofh-histograms.pdf:
python3 src/plot.py ofh-histograms figures/ofh-histograms.pdf
figures/whole-matrix-compute.pdf: plot_data/whole-matrix-compute.csv
python3 src/plot.py whole-matrix-compute plot_data/whole-matrix-compute.csv \
figures/whole-matrix-compute.pdf
figures/whole-matrix-compute-zarr-versions.pdf: plot_data/whole-matrix-compute-zarr-versions.csv
python3 src/plot.py whole-matrix-compute-zarr-versions plot_data/whole-matrix-compute-zarr-versions.csv \
figures/whole-matrix-compute-zarr-versions.pdf
figures/whole-matrix-decode.pdf: plot_data/whole-matrix-decode.csv
python3 src/plot.py whole-matrix-decode plot_data/whole-matrix-decode.csv \
figures/whole-matrix-decode.pdf
figures/column-extract.pdf: plot_data/column-extract.csv
python3 src/plot.py column-extract plot_data/column-extract.csv \
figures/column-extract.pdf
figures/subset-matrix-compute.pdf: plot_data/subset-matrix-compute.csv
python3 src/plot.py subset-matrix-compute plot_data/subset-matrix-compute.csv \
figures/subset-matrix-compute.pdf
figures/subset-matrix-compute-supplemental.pdf: plot_data/subset-matrix-compute.csv
python3 src/plot.py subset-matrix-compute-supplemental \
plot_data/subset-matrix-compute.csv \
figures/subset-matrix-compute-supplemental.pdf
figures/compression-shuffle.pdf: plot_data/shuffle_benchmarks.csv
python3 src/plot.py compression-shuffle \
plot_data/shuffle_benchmarks.csv \
$@
figures/compression-compressor.pdf: plot_data/compressor_benchmarks.csv
python3 src/plot.py compression-compressor \
plot_data/compressor_benchmarks.csv \
$@
figures/compression-chunksize.pdf: plot_data/chunksize_benchmarks.csv
python3 src/plot.py compression-chunksize \
plot_data/chunksize_benchmarks.csv \
$@
figures/compression-chunksize-finegrained.pdf: plot_data/chunksize_finegrained_benchmarks.csv
python3 src/plot.py compression-chunksize-finegrained \
plot_data/chunksize_finegrained_benchmarks.csv \
$@
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 $<