-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathMakefile
95 lines (72 loc) · 3.21 KB
/
Makefile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
nc = 4
rexec = R CMD BATCH --no-save --no-restore
null_plots = ./output/null/exact_null.pdf \
./output/null/likelihood_null.pdf \
./output/null/chi_null.pdf \
./output/null/slrt_null.pdf
alt_plots = ./output/alt/exact_alt.pdf \
./output/alt/likelihood_alt.pdf \
./output/alt/chisqr_alt.pdf \
./output/alt/split_alt.pdf
.PHONY : all
all : sturg alt_sims null_sims small
## Real Data Analysis ----------------------------------------------
.PHONY : sturg
sturg : ./output/sturg/real_qq.pdf
./data/sturg/8n_12n_sturgeon_readCounts.rda :
mkdir -p ./data/sturg
wget --directory-prefix=data/sturg --no-clobber https://datadryad.org/stash/downloads/file_stream/711273
mv ./data/sturg/711273 ./data/sturg/8n_12n_sturgeon_readCounts.rda
./output/sturg/nmat_updog.RDS : ./analysis/real_nmat.R ./data/sturg/8n_12n_sturgeon_readCounts.rda
mkdir -p ./output/rout
mkdir -p ./output/sturg
$(rexec) '--args nc=$(nc)' $< ./output/rout/$(basename $(notdir $<)).Rout
./output/sturg/sims_realdata.RDS : ./analysis/real_fit.R ./output/sturg/nmat_updog.RDS
mkdir -p ./output/rout
mkdir -p ./output/sturg
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout
./output/sturg/real_qq.pdf : ./analysis/real_plot.R ./output/sturg/sims_realdata.RDS
mkdir -p ./output/rout
mkdir -p ./output/sturg
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout
## Null Sims Analysis ----------------------------------------------
.PHONY : null_sims
null_sims : $(null_plots) ./output/null/null_tab.txt
./output/null/sims_out.RDS ./output/null/sims_outtype1.RDS : ./analysis/null_sims.R
mkdir -p ./output/rout
mkdir -p ./output/null
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout
$(null_plots) : ./analysis/null_plot.R ./output/null/sims_out.RDS
mkdir -p ./output/rout
mkdir -p ./output/null
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout
./output/null/null_tab.txt : ./analysis/null_tab.R ./output/null/sims_out.RDS
mkdir -p ./output/rout
mkdir -p ./output/null
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout
## Alt Sims Analysis ----------------------------------------------
.PHONY: alt_sims
alt_sims : $(alt_plots) ./output/alt/alt_tab.txt
./output/alt/sims_alt.RDS : ./analysis/alt_sims.R
mkdir -p ./output/rout
mkdir -p ./output/alt
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout
$(alt_plots) : ./analysis/alt_plot.R ./output/alt/sims_alt.RDS
mkdir -p ./output/rout
mkdir -p ./output/alt
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout
./output/alt/alt_tab.txt : ./analysis/alt_tab.R ./output/alt/sims_alt.RDS
mkdir -p ./output/rout
mkdir -p ./output/alt
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout
## Small Sample Size Data Analysis --------------------------------
.PHONY: small
small : ./output/small/small_hist.pdf
./output/small/sims_samp1.RDS ./output/small/sims_samp2.RDS : ./analysis/small_sims.R
mkdir -p ./output/rout
mkdir -p ./output/small
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout
./output/small/small_hist.pdf : ./analysis/small_plot.R ./output/small/sims_samp1.RDS ./output/small/sims_samp2.RDS
mkdir -p ./output/rout
mkdir -p ./output/small
$(rexec) $< ./output/rout/$(basename $(notdir $<)).Rout