Makefile.docker

# Docker makefile
#
# To build sambamba using a Docker image
#
#   make -f Makefile.docker
#
# To run with the DMD compiler instead:
#
#   make DRUN="dlanguage/dmd dmd" -f Makefile.docker
#
# run with
#
#   ./build/sambamba
#
# Note: you'll need to set the correct LIB_PATHS for libz and libz4 your system


DRUN=dlanguage/ldc ldc2
# Mount the lib search paths on Docker for libz and libz4
LIBZ_LIB_PATH=/gnu/store/yd7bplsvf9nj72wn2z6n38rq9hfmjgd9-zlib-1.2.11/lib
LIBZ4_LIB_PATH=/gnu/store/2n80sdqh39y3sgrfyd97ag0sjx5bx9dl-lz4-1.8.0/lib

CWD=$(shell pwd)
D_COMPILER=docker run -v $(LIBZ_LIB_PATH):$(LIBZ_LIB_PATH) -v $(LIBZ4_LIB_PATH):$(LIBZ4_LIB_PATH) -v $(CWD):/src $(DRUN)

DFLAGS = -wi -I. -IBioD -IundeaD/src
LIBS   = htslib/libhts.a -L-L$(LIBZ4_LIB_PATH) -L-L$(LIBZ_LIB_PATH) -L-L$(LDC_LIB_PATH) -L-L$(CWD)/lib -L-lrt -L-lpthread -L-lm -L-lz -L-llz4
SRC    = $(wildcard main.d utils/*.d thirdparty/*.d cram/*.d) $(wildcard undeaD/src/undead/*.d) $(wildcard BioD/bio/*/*.d BioD/bio/*/*/*.d) $(wildcard sambamba/*.d sambamba/*/*.d sambamba/*/*/*.d)
OBJ    = $(SRC:.d=.o) utils/ldc_version_info_.o
OUT    = build/sambamba

.PHONY: all

debug: DFLAGS += -O0 -g -d-debug -link-debuglib

all: debug

htslib-static:
	cd htslib && $(MAKE)

ldc-version-info:
	./gen_ldc_version_info.py $(shell which ldmd2) > utils/ldc_version_info_.d

utils/ldc_version_info_.o: ldc-version-info
	$(D_COMPILER) $(DFLAGS) -c utils/ldc_version_info_.d -od=$(dir $@)

build-setup: htslib-static ldc-version-info
	mkdir -p build/

guix guix-debug default debug release static profile: $(OUT)

# ---- Compile step
%.o: %.d
	$(D_COMPILER) $(DFLAGS) -c $< -od=$(dir $@)

# ---- Link step
$(OUT): build-setup $(OBJ)
	$(D_COMPILER) $(DFLAGS) -of=build/sambamba $(OBJ) $(LIBS)

test:
	./run_tests.sh

check: test

debug-strip: debug
	objcopy --only-keep-debug build/sambamba sambamba.debug
	objcopy --strip-debug build/sambamba
	objcopy --add-gnu-debuglink=sambamba.debug build/sambamba
	mv sambamba.debug build/

clean-d:
	rm -rf build/*
	rm -f $(OBJ) $(OUT) trace.{def,log}

install:
	install -m 0755 build/sambamba $(prefix)/bin

clean: clean-d
	cd htslib ; make clean