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Makefile
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TEXFILE = Chan_Wardenburg_Staphylococcal_Smooth_Biofilm
#this the the rendered and knit R script to html for browsing intermediate figures and looking at analysis decisions
analysis_html_documentation: *.html
Data/crystal_violet.RData: Data/crystal_violet_biofilm/*
Rscript crystal_violet_datawrangle.R;
rm Rplots.pdf
crystal_violet_datawrangle.html:
Rscript -e "rmarkdown::render(knitr::spin('crystal_violet_datawrangle.R', knit = FALSE), output_dir = 'analysis_html')";
rm crystal_violet_datawrangle.Rmd
crystal_violet_stats_vis.html: Data/crystal_violet.Rdata
Rscript -e "rmarkdown::render(knitr::spin('crystal_violet_stats_vis.R', knit = FALSE), output_dir = 'analysis_html')";
rm crystal_violet_stats_vis.Rmd
crystal_violet_figures:
Rscript crystal_violet_stats_vis.R
rm Rplots.pdf
echo "$@ created, it is a large file..."
crystal_violet_agr_figures:
Rscript crystal_violet_agr_stats_vis.R
rm Rplots.pdf
echo "$@ created, it is a large file..."
Data/hla_psm_tidy.RData: Data/hla/*
Rscript hla_tidy.R
rm Rplots.pdf
Data/merged_raft_cfu.RData: Data/hla_psm_tidy.RData Data/psm_module/* Data/rafts_cfu_merged/*
Rscript rafts_mutants_datawrangle.R
rm Rplots.pdf
rafts_mutants_datawrangle.html:
Rscript -e "rmarkdown::render(knitr::spin('rafts_mutants_datawrangle.R', knit = FALSE), output_dir = 'analysis_html')";
rm rafts_mutants_datawrangle.Rmd
rafts_mutants_stats_vis.html: Data/merged_raft_cfu.RData
Rscript -e "rmarkdown::render(knitr::spin('rafts_mutants_stats_vis.R', knit = FALSE), output_dir = 'analysis_html')";
rm rafts_mutants_stats_vis.Rmd
rafts_agr_stats_vis.html: Data/merged_raft_cfu.RData
Rscript -e "rmarkdown::render(knitr::spin('rafts_agr_stats_vis.R', knit = FALSE), output_dir = 'analysis_html')";
rm rafts_agr_stats_vis.Rmd
rafts_mutants_figures:
Rscript rafts_mutants_stats_vis.R;
rm Rplots.pdf;
echo "$@ created, it is a large file..."
rafts_agr_figures:
Rscript rafts_agr_stats_vis.R;
rm Rplots.pdf;
echo "$@ created, it is a large file..."
Data/cfu_calibration_merged.RData: Data/calibration/*
Rscript calibration_datamerge.R;
rm Rplots.pdf;
echo "$@ created, it is a large file..."
Data/cfu_calibration.RData: Data/cfu_calibration_merged.RData Data/calibration/*
Rscript calibration_datamerge.R;
rm Rplots.pdf;
echo "$@ created, it is a large file..."
cfu_calibration_datawrangle.html:
Rscript -e "rmarkdown::render(knitr::spin('cfu_calibration_datawrangle.R', knit = FALSE), output_dir = 'analysis_html')";
rm cfu_calibration_datawrangle.Rmd
cfu_calibration_figures:
Rscript cfu_calibration_stats_vis.R
rm Rplots.pdf
echo "$@ created, it is a large file..."
Figures/fig1.pdf: cfu_calibration_figures
inkscape Figures/Figure1.svg -A $@;
rm Figures/*.tiff
Figures/fig2.pdf:
inkscape Figures/Figure2.svg -A $@;
rm Figures/*.tiff
Figures/fig3.pdf: rafts_agr_figures
inkscape Figures/Figure3.svg -A $@;
rm Figures/*.tiff
Figures/fig4.pdf: crystal_violet_agr_figures
inkscape Figures/Figure4.svg -A $@;
rm Figures/*.tiff
Figures/figS1.pdf:
inkscape Figures/Supplement_figure1.svg -A $@
Figures/figS2.pdf:
inkscape Figures/Supplement_figure2.svg -A $@
Figures/figS3.pdf: rafts_mutants_figures
inkscape Figures/Supplement_figure3.svg -A $@;
rm Figures/*.tiff
Figures/figS4.pdf:
inkscape Figures/Supplement_figure4.svg -A $@
Figures/figS5.pdf:
inkscape Figures/Supplement_figure5.svg -A $@
Figures/figS6.pdf: crystal_violet_figures
inkscape Figures/Supplement_figure6.svg -A $@;
rm Figures/*.tiff
Figures/%.pdfcrop: Figures/%.pdf
pdfcrop $< $<;
touch $@;
echo "$@ has created and cropped the figure, .pdfcrop token created"
allfigs: mainfigs suppfigs
touch $@;
mainfigs: Figures/fig1.pdf Figures/fig2.pdf Figures/fig3.pdf Figures/fig4.pdf
touch $@;
suppfigs: Figures/figS1.pdf Figures/figS2.pdf Figures/figS3.pdf Figures/figS4.pdf Figures/figS5.pdf Figures/figS6.pdf
touch $@;
$(TEXFILE).pdf: $(TEXFILE).tex
lualatex -interaction nonstopmode -file-line-error $(TEXFILE).tex;
bibtex $(TEXFILE).aux;
lualatex -interaction nonstopmode -halt-on-error -file-line-error $(TEXFILE).tex;
lualatex -interaction nonstopmode -halt-on-error -file-line-error $(TEXFILE).tex;
rm -v $(TEXFILE).blg $(TEXFILE).out $(TEXFILE).aux $(TEXFILE).bbl $(TEXFILE).log