Makefile 5.61 KB
Newer Older
LANORE Vincent's avatar
LANORE Vincent committed
1 2 3 4
# -----------------------------------------------------------------------
#   Build and install things
# -----------------------------------------------------------------------
.PHONY: build
Philippe Veber's avatar
Philippe Veber committed
5 6 7
build:
	jbuilder build

LANORE Vincent's avatar
LANORE Vincent committed
8
.PHONY: install
Philippe Veber's avatar
Philippe Veber committed
9 10
install:
	jbuilder install
11

LANORE Vincent's avatar
LANORE Vincent committed
12
.PHONY: build_docker
13
build_docker:
14
	@for dir in ./etc/docker/*; \
15 16 17
	do\
		cd $${dir}; \
		bash ./build_docker.sh; \
Carine Rey's avatar
Carine Rey committed
18
		cd - ; \
19 20
	done

LANORE Vincent's avatar
LANORE Vincent committed
21
.PHONY: push_docker
22
push_docker:
23
	@for dir in ./etc/docker/*; \
24 25 26
	do\
		cd $${dir}; \
		bash ./build_docker.sh push_yes; \
Carine Rey's avatar
Carine Rey committed
27
		cd - ; \
28
	done
Carine Rey's avatar
Carine Rey committed
29

LANORE Vincent's avatar
LANORE Vincent committed
30
# -----------------------------------------------------------------------
Carine Rey's avatar
Carine Rey committed
31
#   Tests
LANORE Vincent's avatar
LANORE Vincent committed
32 33
# -----------------------------------------------------------------------
.PHONY: test_simu
34
test_simu:
Carine Rey's avatar
Carine Rey committed
35
	cd example && \
36
	reviewphiltrans simulation --outdir outdir --tree-dir trees --profile-fn aa_fitness/tiragesBloomK30.tsv --preview --np 4 && \
37 38
	mv dag.dot dagtest_sim.dot && \
	dot -Tsvg dagtest_sim.dot -o dagtest_sim.svg
39

LANORE Vincent's avatar
LANORE Vincent committed
40
.PHONY: test_det
41 42
test_det:
	cd example && \
Carine Rey's avatar
Carine Rey committed
43
	reviewphiltrans detection --outdir outdir/detection --indir outdir/data --preview --np 4 --fast && \
44 45
	mv dag.dot dagtest_det.dot && \
	dot -Tsvg dagtest_det.dot -o dagtest_det.svg
Carine Rey's avatar
Carine Rey committed
46

LANORE Vincent's avatar
LANORE Vincent committed
47
.PHONY: test_val
Carine Rey's avatar
Carine Rey committed
48 49
test_val:
	cd example && \
Carine Rey's avatar
Carine Rey committed
50
	reviewphiltrans validation --outdir outdir_validation --tree-dir trees --profile-fn aa_fitness/263SelectedProfiles.tsv --preview  --ns 5 --fast --no-ne --np 4 && \
Carine Rey's avatar
Carine Rey committed
51 52 53
	mv dag.dot dagtest_val.dot && \
	dot -Tsvg dagtest_val.dot -o dagtest_val.svg

Carine Rey's avatar
Carine Rey committed
54 55 56 57 58 59 60 61 62 63
# -----------------------------------------------------------------------
#   experiments on real data (only Besnard)
# -----------------------------------------------------------------------
.PHONY: fast_real
fast_real:
	cd example && \
	reviewphiltrans detection --outdir outdir_real_data --indir real_data --fast --np 4 && \
	mv dag.dot dagtest_real.dot && \
	dot -Tpdf dagtest_real.dot -o dagtest_real.pdf

LANORE Vincent's avatar
LANORE Vincent committed
64
.PHONY: real
Carine Rey's avatar
Carine Rey committed
65
real:
Carine Rey's avatar
Carine Rey committed
66
	cd example && \
Carine Rey's avatar
Carine Rey committed
67
	reviewphiltrans detection --outdir outdir_real_data --indir real_data --np 4 && \
Carine Rey's avatar
Carine Rey committed
68 69 70
	mv dag.dot dagtest_real.dot && \
	dot -Tpdf dagtest_real.dot -o dagtest_real.pdf

Carine Rey's avatar
Carine Rey committed
71 72 73
# -----------------------------------------------------------------------
#   experiments on threshold choices
# -----------------------------------------------------------------------
74 75
.PHONY: analyses_we
analyses_we:
Carine Rey's avatar
Carine Rey committed
76
	cd example && \
77 78
	reviewphiltrans validation --outdir outdir_analyses_we --tree-dir trees_analyses_weekend --profile-fn aa_fitness/263SelectedProfiles.tsv --np 28 --ns 1000 && \
	mv dag.dot daganalyses_we.dot
Carine Rey's avatar
Carine Rey committed
79

Carine Rey's avatar
Carine Rey committed
80 81 82
.PHONY: analyses_night
analyses_night:
	cd example && \
Carine Rey's avatar
Carine Rey committed
83 84 85 86 87 88
	reviewphiltrans validation --outdir outdir_analyses_night --tree-dir trees_analyses_night --profile-fn aa_fitness/263SelectedProfiles.tsv --np 27 --ns 100 --fast           && \
	reviewphiltrans validation --outdir outdir_analyses_night --tree-dir trees_analyses_night --profile-fn aa_fitness/263SelectedProfiles.tsv --np 27 --ns 100 --fast --ne-test && \
	reviewphiltrans validation --outdir outdir_analyses_night --tree-dir trees_analyses_night --profile-fn aa_fitness/263SelectedProfiles.tsv --np 27 --ns 100                  && \
	reviewphiltrans validation --outdir outdir_analyses_night --tree-dir trees_analyses_night --profile-fn aa_fitness/263SelectedProfiles.tsv --np 27 --ns 100        --ne-test && \
	mv dag.dot dag_analyses_night.dot

Carine Rey's avatar
Carine Rey committed
89

Carine Rey's avatar
Carine Rey committed
90 91 92 93 94 95
.PHONY: analyses_night2
analyses_night2:
	cd example && \
	reviewphiltrans validation --outdir outdir_analyses_night2_ne_test --tree-dir trees_analyses_night2 --profile-fn aa_fitness/263SelectedProfiles.tsv --np 28 --ne-test --ns 100 --fast && \
	reviewphiltrans validation --outdir outdir_analyses_night2         --tree-dir trees_analyses_night2 --profile-fn aa_fitness/263SelectedProfiles.tsv --np 28           --ns 100 && \
	reviewphiltrans validation --outdir outdir_analyses_night2_ne_test --tree-dir trees_analyses_night2 --profile-fn aa_fitness/263SelectedProfiles.tsv --np 28 --ne-test --ns 100 && \
Carine Rey's avatar
Carine Rey committed
96
	mv dag.dot dag_analyses_night2.dot
Carine Rey's avatar
Carine Rey committed
97

Carine Rey's avatar
Carine Rey committed
98 99 100
.PHONY: analyses_night3
analyses_night3:
	cd example && \
Carine Rey's avatar
Carine Rey committed
101 102
	reviewphiltrans validation --outdir outdir_analyses_night3_ne_test --tree-dir trees_analyses_night3 --profile-fn aa_fitness/263SelectedProfiles.tsv --np 28 --ne-test --ns 100 --fast && \
	reviewphiltrans validation --outdir outdir_analyses_night3_ne_test --tree-dir trees_analyses_night3 --profile-fn aa_fitness/263SelectedProfiles.tsv --np 28            --ns 100       && \
Carine Rey's avatar
Carine Rey committed
103 104 105
	reviewphiltrans validation --outdir outdir_analyses_night3_ne_test --tree-dir trees_analyses_night3 --profile-fn aa_fitness/263SelectedProfiles.tsv --np 28 --ne-test --ns 100 && \
	mv dag.dot dag_analyses_night3.dot

Carine Rey's avatar
Carine Rey committed
106

Carine Rey's avatar
update  
Carine Rey committed
107 108
.PHONY: analyses_night5
analyses_night5:
Carine Rey's avatar
Carine Rey committed
109
	cd example && \
Carine Rey's avatar
update  
Carine Rey committed
110 111 112
	reviewphiltrans validation --outdir outdir_analyses_night5 --tree-dir trees_analyses_night --profile-fn aa_fitness/263SelectedProfiles.tsv --preview --np 28 --no-ne --no-hapc --ns 200 --fast && \
	reviewphiltrans validation --outdir outdir_analyses_night5 --tree-dir trees_analyses_night --profile-fn aa_fitness/263SelectedProfiles.tsv           --np 28 --no-ne --no-hapc --ns 200 --fast && \
	reviewphiltrans validation --outdir outdir_analyses_night5 --tree-dir trees_analyses_night --profile-fn aa_fitness/263SelectedProfiles.tsv           --np 28 --no-ne --no-hapc --ns 200        && \
Carine Rey's avatar
Carine Rey committed
113 114
	mv dag.dot dag_analyses_night4.dot

LANORE Vincent's avatar
LANORE Vincent committed
115 116 117 118 119 120 121 122 123 124
# -----------------------------------------------------------------------
#   Cleaning and formatting
# -----------------------------------------------------------------------
.PHONY: clean
clean:
	rm -rf _build
	rm -rf example/_bistro
	rm -rf example/outdir

.PHONY: clean_test
Carine Rey's avatar
Carine Rey committed
125
clean_test:
126 127 128 129
	rm -rf example/_bistro
	rm -rf example/outdir
	rm -rf example/report.log
	rm -rf example/dot.dag
130

LANORE Vincent's avatar
LANORE Vincent committed
131
.PHONY: format
132 133
format:
	ocp-indent -i lib/*.ml lib/*.mli app/*.ml