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Makefile
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nc = 6
rexec = R CMD BATCH --no-save --no-restore
simsout = ./output/sims/null_sims_g.csv \
./output/sims/null_sims_gl.csv \
./output/sims/alt_sims_g.RDS \
./output/sims/alt_sims_gl.RDS
chisq_plots = ./output/sims/chisq//ucsq_g_01.pdf \
./output/sims/chisq//ucsq_g_02.pdf \
./output/sims/chisq//ucsq_g_11.pdf \
./output/sims/chisq//ucsq_g_12.pdf \
./output/sims/chisq//ucsq_gl_rd10_01.pdf \
./output/sims/chisq//ucsq_gl_rd10_02.pdf \
./output/sims/chisq//ucsq_gl_rd10_11.pdf \
./output/sims/chisq//ucsq_gl_rd10_12.pdf \
./output/sims/chisq//ucsq_gl_rd10_22.pdf \
./output/sims/chisq//ucsq_gl_rd100_01.pdf \
./output/sims/chisq//ucsq_gl_rd100_02.pdf \
./output/sims/chisq//ucsq_gl_rd100_11.pdf \
./output/sims/chisq//ucsq_gl_rd100_12.pdf \
./output/sims/chisq//ucsq_gl_rd100_22.pdf
pm_plots = ./output/sims/pm/null_g_pmalpha_box.pdf \
./output/sims/pm/null_gl_pmalpha_box.pdf
bf_plots = ./output/sims/bf/alt_g_boxplot.pdf \
./output/sims/bf/alt_gl_boxplot.pdf \
./output/sims/bf/null_g_boxplot.pdf \
./output/sims/bf/null_gl_boxplot_rd10.pdf \
./output/sims/bf/null_gl_boxplot_rd100.pdf
blueplots = ./output/blue/bad_diff.pdf \
./output/blue/bad_snps.pdf \
./output/blue/blue_logbf_hist.pdf \
./output/blue/blue_qq.pdf \
./output/blue/chr_dr_scatter.pdf
.PHONY : all
all : blue sims
# Blueberry analysis ----
.PHONY : blue
blue : $(blueplots)
./output/blue/bluefits.RDS : ./code/blue_up.R ./data/updog_input_240ind_Sweet_Indi.Rdata
mkdir -p ./output/rout
mkdir -p ./output/blue
$(rexec) '--args nc=$(nc)' $< ./output/rout/$(basename $(notdir $<)).Rout
./output/blue/blue_df.csv : ./code/blue_test.R ./output/blue/bluefits.RDS
mkdir -p ./output/rout
mkdir -p ./output/blue
$(rexec) '--args nc=$(nc)' $< ./output/rout/$(basename $(notdir $<)).Rout
$(blueplots) : ./code/blue_plots.R ./output/blue/blue_df.csv
mkdir -p ./output/rout
mkdir -p ./output/sims
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout
# Sims ----
.PHONY : sims
sims : $(chisq_plots) $(pm_plots) $(bf_plots)
./output/sims/null_sims_g.csv : ./code/null_sims_g.R
mkdir -p ./output/rout
mkdir -p ./output/sims
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout
./output/sims/null_sims_gl.csv : ./code/null_sims_gl.R
mkdir -p ./output/rout
mkdir -p ./output/sims
$(rexec) '--args nc=$(nc)' $< ./output/rout/$(basename $(notdir $<)).Rout
./output/sims/alt_sims_g.RDS : ./code/alt_sims_g.R
mkdir -p ./output/rout
mkdir -p ./output/sims
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout
./output/sims/alt_sims_gl.RDS : ./code/alt_sims_gl.R
mkdir -p ./output/rout
mkdir -p ./output/sims
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout
$(chisq_plots) : ./code/chisq_plots.R $(simsout)
mkdir -p ./output/rout
mkdir -p ./output/sims
mkdir -p ./output/sims/chisq
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout
$(pm_plots) : ./code/pm_plots.R $(simsout)
mkdir -p ./output/rout
mkdir -p ./output/sims
mkdir -p ./output/sims/pm
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout
$(bf_plots) : ./code/sim_plots.R $(simsout)
mkdir -p ./output/rout
mkdir -p ./output/sims
mkdir -p ./output/sims/bf
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout