Makefile.guix

# GNU Guix dev makefile. GNU Guix is the package manager for GNU and we
# use it for sambamba development and deployment. Normally use the
# standard Makefile instead because it compiles into a singleobj which
# gives better performance. This Makefile is for development purposes.
#
# But it is preferred to run in a Guix environment/container. For more
# information see INSTALL.md

D_COMPILER=ldc2
CC=gcc
CPP=gcc
BIOD_PATH=./BioD:./BioD/contrib/msgpack-d/src

# DLIBS       = $(LIBRARY_PATH)/libphobos2-ldc.a $(LIBRARY_PATH)/libdruntime-ldc.a
# DLIBS_DEBUG = $(LIBRARY_PATH)/libphobos2-ldc-debug.a $(LIBRARY_PATH)/libdruntime-ldc-debug.a


DFLAGS = -wi -I. -I$(BIOD_PATH) -J.
# DLIBS  = $(LDC_LIB_PATH)/libphobos2-ldc.a $(LDC_LIB_PATH)/libdruntime-ldc.a
# DLIBS_DEBUG = -debuglib=phobos2-ldc-debug,druntime-ldc-debug $(LDC_LIB_PATH)/libphobos2-ldc-debug.a $(LDC_LIB_PATH)/libdruntime-ldc-debug.a -link-debuglib
# DLIBS_DEBUG = -debuglib=phobos2-ldc-debug-shared,druntime-ldc-debug-shared -link-debuglib -L-lphobos2-ldc-debug-shared -L-ldruntime-ldc-debug-shared
# RPATH  = -L--rpath=$(dir $(realpath $(LDC_LIB_PATH)/libz.so)):$(dir $(realpath $(LDC_LIB_PATH)/liblz4.so))
RPATH = -L--rpath=$(LIBRARY_PATH)
LIBS   = -L-L$(LDC_LIB_PATH) -L-lrt -L-lpthread -L-lm -L-lz -L-llz4

LIBS_STATIC = $(DLIBS) -L-lz -L-llz4 -L-lphobos2-ldc -L-ldruntime-ldc -L-lldc-jit-rt
SRC         = $(wildcard main.d utils/*.d thirdparty/*.d) $(wildcard BioD/contrib/undead/*.d BioD/contrib/undead/*/*.d) $(wildcard BioD/bio/*/*.d BioD/bio/*/*/*.d BioD/bio/*/*/*/*.d BioD/bio/*/*/*/*/*.d BioD/bio/*/*/*/*/*/*/*.d BioD/contrib/msgpack-d/src/msgpack/*.d) $(wildcard sambamba/*.d sambamba/*/*.d sambamba/*/*/*.d)
OBJ    = $(SRC:.d=.o)
OUT    = bin/sambamba-$(shell cat VERSION)
static: OUT += -static

.PHONY: all guix guix-debug debug release static profile clean test

# The Guix targets resolve the RPATH automatically
guix:        DFLAGS += -O -release -g # Guix strips debug flags

guix-debug:  DFLAGS += -O0 -g -d-debug -unittest

# The following options are run in development from ~/.guix-profile and need to inject the RPATH
debug:              DFLAGS += -O0 -g -d-debug $(RPATH) -link-debuglib -unittest

release static:     DFLAGS += -O3 -release $(RPATH) -enable-inlining -Hkeep-all-bodies -boundscheck=off

static:             DFLAGS += -static -L-Bstatic -L-L/gnu/store/rmjlycdgiq8pfy5hfi42qhw3k7p6kdav-glibc-2.25/lib/

profile:            DFLAGS += -g -O -fprofile-instr-generate=profile.raw $(RPATH)

profile:            LIBS += -L=-lprofile_rt

guix release:       LIBS += $(DLIBS)

static:             LIBS = $(LIBS_STATIC)

guix-debug debug profile: LIBS += $(DLIBS_DEBUG)

all: debug

# bio2/pileup.d: bio2/bam/reader.d

# sambamba/subsample.d: bio2/pileup.d

utils/ldc_version_info_.d:
	python ./gen_ldc_version_info.py $(shell which ldmd2) > utils/ldc_version_info_.d
	cat utils/ldc_version_info_.d

ldc_version_info: utils/ldc_version_info_.d

build-setup: ldc_version_info
	mkdir -p bin/

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

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

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

# ---- Link step
$(OUT): $(OBJ)
	mkdir -p bin/
	$(D_COMPILER) $(DFLAGS) -of=$(OUT) $(OBJ) $(LIBS)

test:	clean-tests
	./run_tests.sh $(OUT)

biod:
	cd $(BIOD_PATH)/src_ragel && make

check: all debug test

debug-strip: debug
	objcopy --only-keep-debug $(OUT) sambamba.debug
	objcopy --strip-debug $(OUT)
	objcopy --add-gnu-debuglink=sambamba.debug $(OUT)
	mv sambamba.debug bin/

install:
	install -m 0755 $(OUT) $(prefix)/bin

clean-c:

clean-d:
	rm -v $(OBJ) $(OUT) # trace.{def,log}
	rm -v bin/*

clean-tests:
	rm -rf output/*

clean: clean-c clean-d clean-tests