Skeleton of a Makefile

skeleton.mk

SHELL = /bin/bash

DDIR = data
RDIR = results
SDIR = src

SAMPLES = S1 S2 S3
DOUBLED_SAMPLES = $(foreach sample, $(SAMPLES), $(sample)/$(sample))

####################
# BEAUTY TARGETS
#########################
.PHONY: all

all:

get_data: $(addprefix $(DDIR)/, $(SAMPLES:=.tar.gz))
run_program: $(addprefix $(RDIR)/program/, $(DOUBLED_SAMPLES:=.new.fa))

####################
# ACTUAL TARGETS
####################
$(DDIR)/%.gz:
  mkdir -p $(dir $@)
	wget URL/$*.tar.gz -O $@

.SECONDEXPANSION:
$(RDIR)/program/%.new.fa: $(DDIR)/$$(notdir $$*).fa
	@echo "###### RUNNING program - $(notdir $*) ######"
	@date
	mkdir -p $(dir $@)
	(date &&\
	$(PROGRAM_BIN) -i $^ -o $@ &&\
	date) 2>$(dir $@)/program.stderr 1>$(dir $@)/program.stdout
	@date
	@echo "##########"
	@echo

####################
# CLEAN-UP
####################
clean:
	@echo "TODO: clean"