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Makefile
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Makefile
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R_OPTS=--no-save --no-restore --no-init-file --no-site-file # --vanilla, but without --no-environ
STEM = magic2019
FIGS = Figs/rqtl_lines_code.pdf \
Figs/phefile.pdf \
Figs/geno_reconstruct.pdf \
Figs/scan_hk.pdf \
Figs/snp_asso.pdf \
Figs/coef_fl.pdf
docs/$(STEM).pdf: $(STEM).pdf
cp $< $@
$(STEM).pdf: $(STEM).tex header.tex $(FIGS)
xelatex $<
web: $(STEM).pdf
scp $(STEM).pdf adhara.biostat.wisc.edu:Website/presentations/$(STEM).pdf
Figs/rqtl_lines_code.pdf: R/rqtl_lines_code.R R/colors.R Data/lines_code_by_version.csv
cd $(<D);R CMD BATCH $(R_OPTS) $(<F)
Figs/phefile.pdf: R/data_files_fig.R
cd $(<D);R CMD BATCH $(R_OPTS) $(<F)
Figs/geno_reconstruct.pdf: R/geno_reconstruct_fig.R
cd $(<D);R CMD BATCH $(R_OPTS) $(<F)
Figs/scan_hk.pdf: R/scans_fig.R
cd $(<D);R CMD BATCH $(R_OPTS) $(<F)
Figs/snp_asso.pdf: R/snp_asso_fig.R Figs/scan_hk.pdf
cd $(<D);R CMD BATCH $(R_OPTS) $(<F)
Figs/coef_fl.pdf: R/coef_fig.R Figs/scan_hk.pdf
cd $(<D);R CMD BATCH $(R_OPTS) $(<F)
Data/lines_code_by_version.csv: Perl/grab_lines_code.pl Data/versions.txt
cd Perl;grab_lines_code.pl
Figs/magic19_scan.pdf: R/magic19_figs.R R/colors.R
cd $(<D);R $(R_OPTS) -e "source('$(<F)')"