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Makefile
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#!/bin/bash
# Define commands
RDATA=R CMD BATCH --vanilla $< logs/$(<F).Rout
all: data/gene_annotations.rds \
data/mf_annotations.rds \
data/model_hm.rds \
data/model_factors_short.rds \
data/model_factors_long.rds \
data/differential_expression.rds \
data/binding_peaks.rds \
data/gene_set_enrichment.rds \
data/peaks_overlap_enrichment.rds \
data/targets_over_representation.rds \
data/molecular_functions_overrepresentation.rds \
manuscript.pdf
data/gene_annotations.rds: scripts/gene_annotations.R
$(RDATA)
data/mf_annotations.rds: scripts/mf_annotations.R \
data/gene_annotations.rds
$(RDATA)
data/model_hm.rds: scripts/model_hm.R \
$(bash find data/mm10/*) \
$(bash find data/segmentation/hm/bins_200/*)
$(RDATA)
data/model_factors_short.rds: scripts/model_factors_short.R \
$(bash find data/mm10/*) \
$(bash find data/segmentation/factors_short/bins_200/*)
$(RDATA)
data/model_factors_long.rds: scripts/model_factors_long.R \
$(bash find data/mm10/*) \
$(bash find data/segmentation/factors_long/bins_200/*)
$(RDATA)
data/differential_expression.rds: scripts/differential_expression.R \
data/adipo_counts.rds \
data/counts_cebpb_kd.rds \
data/arrays_pparg_kd.rds
$(RDATA)
data/binding_peaks.rds: scripts/binding_peaks.R \
data/segmentation/input_files_factors_long.tsv \
data/segmentation/input_files_factors_short.tsv \
$(bash find data/peaks/*)
$(RDATA)
data/gene_set_enrichment.rds: scripts/gene_set_enrichment.R \
data/differential_expression.rds \
data/gene_annotations.rds \
data/binding_peaks.rds
$(RDATA)
data/peaks_overlap_enrichment.rds: scripts/peaks_overlap_enrichment.R \
data/binding_peaks.rds
$(RDATA)
data/targets_over_representation.rds: scripts/targets_over_representation.R \
data/gene_annotations.rds \
data/binding_peaks.rds
$(RDATA)
data/molecular_functions_overrepresentation.rds: scripts/molecular_functions_overrepresentation.R \
data/gene_annotations.rds \
data/mf_annotations.rds \
data/binding_peaks.rds
$(RDATA)
manuscript.pdf: manuscript.Rmd \
$(bash find data/*)
Rscript -e 'rmarkdown::render("manuscript.Rmd")'