Makefile.RPTOR

## Makefile for autogenerating analysis and figures for RPTOR paper...

# Source data
ALL_EXPR = data/all_gene_expression.tsv
CTRL_GENO = data/control_FLG_genotypes.dat
CASE_GENO = data/eczema_FLG_genotypes.dat
CASE_EXPR = data/eczema_gene_expression.tsv

# Output to be generated
GENE ?= RPTOR
GENEID:=$(shell grep "$(GENE)\b" $(ALL_EXPR) | cut -f 1)
FIG = $(GENE)_boxplot.pdf
COR = $(GENE)_correlation_eczema.tsv
ANNOT = $(GENE)_correlation_eczema_annotated.tsv

VERSION = 0.7

.PHONY: clean reallyclean figures  all version

all: figures

figures: $(FIG) $(ANNOT)
	@echo "Creating figures - Done!"

## Plot filaggrin gene expression across cases and controls stratified by genotype
$(FIG): bin/plot_expression_boxplot.R $(ALL_EXPR) $(CTRL_GENO) $(CASE_GENO)
	Rscript bin/plot_expression_boxplot.R $(ALL_EXPR) $(CTRL_GENO) $(CASE_GENO) $(GENE) 

## Perform filaggrin gene expression correlation analysis 
$(COR): bin/FLG_correlation_analysis.R $(CASE_EXPR) $(CASE_GENO)
	Rscript bin/FLG_correlation_analysis.R $(CASE_EXPR) $(CASE_GENO) $(GENE)_correlation_eczema $(GENEID) 25

## annotate output with Ensembl info, if script available
$(ANNOT): $(COR)
	@which -s add_gene_name_column.pl && add_gene_name_column.pl --in $< --species human --delim ',' --desc --info-col 1 --out $@ || echo "Note: although not critical, the add_gene_name_column.pl script was not found. It can be downloaded from here: https://github.com/drchriscole/ensemblUtils" 

## report version of make file and scripts
version:
	@echo "Makefile version: $(VERSION)"
	Rscript bin/plot_expression_boxplot.R --version
	Rscript bin/FLG_correlation_analysis.R --version

## remove output files
clean:
	rm -f $(GENE)*.pdf $(GENE)*.tsv

reallyclean:
	rm -f *.pdf *.tsv