Makefile

# ==========================
# BEDTools Makefile
# (c) 2009 Aaron Quinlan
# ==========================

# define our object and binary directories
export OBJ_DIR  = obj
export BIN_DIR  = bin
export SRC_DIR  = src
export CXX      = g++
export CXXFLAGS = -Wall -O2
export LIBS     = -lz

SUBDIRS = $(SRC_DIR)/bamToBed \
          $(SRC_DIR)/bedToBam \
          $(SRC_DIR)/bedToIgv \
          $(SRC_DIR)/bed12ToBed6 \
          $(SRC_DIR)/closestBed \
          $(SRC_DIR)/complementBed \
          $(SRC_DIR)/coverageBed \
          $(SRC_DIR)/fastaFromBed \
          $(SRC_DIR)/genomeCoverageBed \
          $(SRC_DIR)/groupBy \
          $(SRC_DIR)/intersectBed \
          $(SRC_DIR)/linksBed \
          $(SRC_DIR)/maskFastaFromBed \
          $(SRC_DIR)/mergeBed   \
          $(SRC_DIR)/overlap \
          $(SRC_DIR)/pairToBed \
          $(SRC_DIR)/pairToPair \
          $(SRC_DIR)/shuffleBed \
          $(SRC_DIR)/slopBed \
          $(SRC_DIR)/sortBed \
          $(SRC_DIR)/subtractBed \
          $(SRC_DIR)/unionBedGraphs \
          $(SRC_DIR)/windowBed

UTIL_SUBDIRS =  $(SRC_DIR)/utils/lineFileUtilities \
                $(SRC_DIR)/utils/bedFile \
                $(SRC_DIR)/utils/tabFile \
                $(SRC_DIR)/utils/genomeFile \
                $(SRC_DIR)/utils/gzstream \
                $(SRC_DIR)/utils/fileType \
                $(SRC_DIR)/utils/bedFilePE \
                $(SRC_DIR)/utils/sequenceUtilities \
                $(SRC_DIR)/utils/BamTools

all:

	@echo "Building BEDTools:"
	@echo "========================================================="
	
	@for dir in $(UTIL_SUBDIRS); do \
		echo "- Building in $$dir"; \
		$(MAKE) --no-print-directory -C $$dir; \
		echo ""; \
	done

	@for dir in $(SUBDIRS); do \
		echo "- Building in $$dir"; \
		$(MAKE) --no-print-directory -C $$dir; \
		echo ""; \
	done


.PHONY: all

clean:
	@echo "Cleaning up."
	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*

.PHONY: clean