https://github.com/sfu-compbio/mrsfast
Tip revision: f47ff337f20dc88f2ae1a9bfdb2a7596d202cfd2 authored by Iman Sarrafi on 06 August 2014, 21:49:44 UTC
README.md edited online with Bitbucket
README.md edited online with Bitbucket
Tip revision: f47ff33
Makefile
DEBUG := 0
PROFILE := 0
MRSFAST_VERSION := "3.3.2"
BUILD_DATE := "$(shell date)"
all: OPTIMIZE_FLAGS build
debug: DEBUG_FLAGS build
profile: PROFILE_FLAGS build
build: clean-executable SSE_FLAGS compile mrsfast snp_indexer clean
LDFLAGS=#-static
LIBS=-lz -lm -pthread -lpthread
CFLAGS=-fno-pic -DMRSFAST_VERSION=\"$(MRSFAST_VERSION)\" -DBUILD_DATE=\"$(BUILD_DATE)\"
objects=baseFAST.o Sort.o MrsFAST.o Common.o CommandLineParser.o RefGenome.o HashTable.o Reads.o Output.o SNPReader.o HELP.o
compile: $(objects)
mrsfast:
ifeq ($(shell uname -s),Linux)
gcc -w $(objects) -o $@ ${LDFLAGS} ${LIBS}
else
gcc -Wl,-no_pie -fno-pic -w $(objects) -o $@ ${LDFLAGS} ${LIBS}
endif
snp_indexer: SNPIndexer.o
gcc $^ -o $@ ${LDFLAGS} ${LIBS}
clean:
@rm -f $(objects)
@rm -f SNPIndexer.o
@rm -f HELPstub.c
@rm -f HELPstub.o
clean-executable:
@rm -f mrsfast
HELP.o:
@groff -Tascii -man ./HELP.man > HELP
ifeq ($(shell uname -s),Linux)
@ld -r -b binary -o HELP.o HELP
else
@touch HELPstub.c
gcc -o HELPstub.o -c HELPstub.c
ld -r -o HELP.o -sectcreate binary HELP HELP HELPstub.o
endif
DEBUG_FLAGS:
$(eval CFLAGS = $(CFLAGS) -ggdb)
$(eval LIBS = $(LIBS) -ggdb)
OPTIMIZE_FLAGS:
$(eval CFLAGS = $(CFLAGS) -O2)
PROFILE_FLAGS:
$(eval CFLAGS = $(CFLAGS) -pg -g)
$(eval LIBS = $(LIBS) -pg -g)
SSE_FLAGS:
ifeq ($(shell uname -s),Linux)
ifeq ($(with-sse4),no)
$(shell echo "-DSSE4=0")
else
$(eval CFLAGS = $(CFLAGS) \
$(shell gv=`gcc -dumpversion`; \
sc=`grep -c "sse4" /proc/cpuinfo`; \
echo $$sc.$$gv | awk -F. '{if($$1>0 && $$2>=4 && $$3>=4) print "-DSSE4=1 -msse4.2"; else print "-DSSE4=0"}'))
endif
else
ifeq ($(with-sse4),no)
$(shell echo "-DSSE4=0")
else
$(eval CFLAGS = $(CFLAGS) \
$(shell gv=`gcc -dumpversion`; \
sc=`sysctl -n machdep.cpu.features | grep -c "SSE4"` ;\
echo $$sc.$$gv | awk -F. '{if($$1>0 && $$2>=4 && $$3>=4) print "-DSSE4=1 -msse4.2"; else print "-DSSE4=0"}'))
endif
endif