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Makefile
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Makefile
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# Lists o' targets
RAWGELS := $(notdir $(wildcard rawdata/GelDoc/*.tif))
GELS := $(addprefix data/GelDoc/,$(subst tif,jpg,$(RAWGELS)))
# RAWQPCR = \
# rawdata/qpcr/admin_2015-03-19_20-49-05_BR003082_prairie16s-Melt_Curve_RFU_Results_SYBR.csv \
# rawdata/qpcr/2015-03-19_platekey.csv \
# rawdata/qpcr/admin_2015-04-21_19-36-12_BR003082_Prairie16s-Melt_Curve_RFU_Results_SYBR.csv \
# rawdata/qpcr/2015-04-21_platekey.csv
NANODROP = data/nanodrop.csv \
figs/ctab_yield.pdf
# QPCR = data/multi_ctab_melt_summary-20150319.csv \
# data/multi_ctab_melt_curves-20150319.csv \
# data/multi_ctab_melt_distance_ordresults-20150319.txt \
# figs/multi_ctab_peakfit-20150319.pdf \
# figs/multi_ctab_melt_npeak_tm-20150319.pdf \
# figs/multi_ctab_melt_curves-20150319.pdf \
# figs/multi_ctab_melt_distance-20150319.pdf \
QPCR = data/multi_ctab_melt_summary-20150421.csv \
data/multi_ctab_melt_curves-20150421.csv \
data/multi_ctab_melt_distance_ordresults-20150421.txt \
figs/multi_ctab_peakfit-20150421.pdf \
figs/multi_ctab_melt_npeak_tm-20150421.pdf \
figs/multi_ctab_melt_curves-20150421.pdf \
figs/multi_ctab_melt_distance-20150421.pdf
TEXTURE = figs/mass_texture.pdf
SEQPLOTS = figs/mock_gen.pdf \
data/aboveground_abundance.txt \
figs/agbg_genblock.pdf \
figs/h2o.pdf \
figs/spikes.pdf \
figs/genus_depth.pdf \
figs/family_depth.pdf \
figs/ordination.pdf \
data/adonis_out.txt \
figs/cooccur_obs_exp.pdf \
figs/cooccur_effect.pdf
ALL = $(GELS) $(NANODROP) $(QPCR) $(TEXTURE) $(SEQPLOTS)
# Phony rules to let us build subsets by themselves
all: $(ALL)
nanodrop: $(NANODROP)
gels: $(GELS)
qpcr: $(QPCR)
clean: rm $(ALL)
.PHONY: all gels nanodrop qpcr clean
# Now for the rules that actually build things
data/GelDoc/%.jpg: \
Python/gel-labeler.py \
rawdata/GelDoc/%.tif \
rawdata/GelDoc/%.csv
./$^ $@
data/nanodrop.csv: \
R/nanodrop_clean.R \
rawdata/nanodrop/*.txt \
rawdata/nanodrop/nanodrop_corrections.csv
Rscript R/nanodrop_clean.R rawdata/nanodrop/*.txt
figs/ctab_yield.pdf: \
R/ctab_yield.R \
data/nanodrop.csv
Rscript $^
# FIXME: All the qpcr scripts contain hardcoded output paths
# These are currently set to write the 2015-04-21 files;
# to run 2014-03-19 files either change paths everywhere and change which blocks are commented in the Makefile
# or better yet FIXME FIXME FIXME.
# data/multi_ctab_melt_summary-20150319.csv \
# data/multi_ctab_melt_curves-20150319.csv \
# figs/multi_ctab_peakfit-20150319.pdf: \
# R/qpcr_curve.R \
# rawdata/qpcr/admin_2015-03-19_20-49-05_BR003082_prairie16s-Melt_Curve_RFU_Results_SYBR.csv \
# rawdata/qpcr/2015-03-19_platekey.csv
# Rscript $^
data/multi_ctab_melt_summary-20150421.csv \
data/multi_ctab_melt_curves-20150421.csv \
figs/multi_ctab_peakfit-20150421.pdf: \
R/qpcr_curve.R \
rawdata/qpcr/admin_2015-04-21_19-36-12_BR003082_Prairie16s-Melt_Curve_RFU_Results_SYBR.csv \
rawdata/qpcr/2015-04-21_platekey.csv
Rscript $^
# figs/multi_ctab_melt_npeak_tm-20150319.pdf: \
# R/plot_melt_summary.R \
# data/multi_ctab_melt_summary-20150319.csv
# Rscript $^
figs/multi_ctab_melt_npeak_tm-20150421.pdf: \
R/plot_melt_summary.R \
data/multi_ctab_melt_summary-20150421.csv
Rscript $^
# figs/multi_ctab_melt_curves-20150319.pdf: \
# R/plot_melt_curve.R \
# data/multi_ctab_melt_curves-20150319.csv
# Rscript $^
figs/multi_ctab_melt_curves-20150421.pdf: \
R/plot_melt_curve.R \
data/multi_ctab_melt_curves-20150421.csv
Rscript $^
# figs/multi_ctab_melt_distance-20150319.pdf data/multi_ctab_melt_distance_ordresults-20150319.txt: \
# R/plot_melt_distance.R \
# data/multi_ctab_melt_curves-20150319.csv
# Rscript $^
figs/multi_ctab_melt_distance-20150421.pdf data/multi_ctab_melt_distance_ordresults-20150421.txt: \
R/plot_melt_distance.R \
data/multi_ctab_melt_curves-20150421.csv
Rscript $^
figs/mass_texture.pdf: R/plot_texture.R rawdata/giddings_rootmass.csv rawdata/soil_properties_2008.csv
Rscript R/plot_texture.R
$(SEQPLOTS): R/plot_seqs.R \
rawdata/bulk_CN.csv \
data/plant_its2_otu/plant_its2_99.biom \
rawdata/vouchers/root_voucher_fate.csv \
rawdata/vouchers/accepted_names.csv \
private/Xiaohui_species_comp/surveys_clean.csv
Rscript R/plot_seqs.R