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Makefile
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# Data setup
data/hsal:
cd data/raw/hsal; python parse.py
data/paer:
cd data/raw/paer; python parse.py
data: data/paer data/hsal
.PHONY: data data/paer data/hsal
# Posterior inference
models := mnull mbatch mfull
# core recipes
sampling/hsalinarum/combined/%/posterior_0.pkl:
cd sampling;\
mkdir -p hsalinarum/combined/$*/;\
python hsalinarum.py $(word 4, $(subst /, ,$(@D))) $(word 5, $(subst /, ,$(@D))) \
--adapt_delta=0.95 --max_treedepth=20 \
> hsalinarum/combined/$*/log.out \
2> hsalinarum/combined/$*/log.err
sampling/hsalinarum/individual/%/posterior_0.pkl:
cd sampling;\
mkdir -p hsalinarum/individual/$*/;\
python hsalinarum.py $(word 4, $(subst /, ,$(@D))) mnull \
--dataset $(word 5, $(subst /, ,$(@D))) \
--adapt_delta=0.95 --max_treedepth=20 \
> hsalinarum/individual/$*/log.out \
2> hsalinarum/individual/$*/log.err
sampling/paeruginosa/combined/%/posterior_0.pkl:
cd sampling;\
mkdir -p paeruginosa/combined/$*/;\
python paeruginosa.py $(word 4, $(subst /, ,$(@D))) $(word 5, $(subst /, ,$(@D))) \
--adapt_delta=0.95 --max_treedepth=15 \
> paeruginosa/combined/$*/log.out \
2> paeruginosa/combined/$*/log.err
sampling/paeruginosa/individual/%/posterior_0.pkl:
cd sampling;\
mkdir -p paeruginosa/individual/$*/;\
python paeruginosa.py $(word 4, $(subst /, ,$(@D))) mnull \
--dataset $(word 5, $(subst /, ,$(@D))) \
--adapt_delta=0.95 --max_treedepth=15 \
> paeruginosa/individual/$*/log.out \
2> paeruginosa/individual/$*/log.err
# H. salinarum
conditions := low hi
hbatches := $(foreach batch,$(wildcard data/hi-oxidative/*),$(lastword $(subst /, ,$(batch))))
hsalCombined: $(foreach cond,$(conditions),$(foreach model,$(models),sampling/hsalinarum/combined/$(cond)/$(model)/samples/posterior_0.pkl))
hsalIndiv: $(foreach cond,$(conditions),$(foreach batch,$(hbatches),sampling/hsalinarum/individual/$(cond)/$(batch)/samples/posterior_0.pkl))
hsal: hsalCombined hsalIndiv
.PHONY: hsalCombined hsalIndiv hsal
# P. aeruginosa
acids := benzoate citric malic
paerCombined: $(foreach acid,$(acids),$(foreach model,$(models),sampling/paeruginosa/combined/$(acid)/$(model)/samples/posterior_0.pkl))
paerIndiv: sampling/paeruginosa/individual/benzoate/PA01_Benzoate_15_min_time_points/samples/posterior_0.pkl sampling/paeruginosa/individual/benzoate/PA01_Benzoate_repeat_19.07.17/samples/posterior_0.pkl sampling/paeruginosa/individual/malic/PA01_Malic_09.03.17/samples/posterior_0.pkl sampling/paeruginosa/individual/malic/PA01_Malic_repeat_27.07.17/samples/posterior_0.pkl sampling/paeruginosa/individual/citric/PA01_citric_15_min_time_points_06.03.17/samples/posterior_0.pkl sampling/paeruginosa/individual/citric/PA01_Citric_rerun_11.07.17/samples/posterior_0.pkl
paer: paerCombined paerIndiv
.PHONY: paer paerCombined paerIndiv
all: paer hsal
.PHONY: all