https://github.com/sfu-compbio/mrsfast
Revision f380a5b33b7e915f14b16e9c2fcda187d8753936 authored by Iman Sarrafi on 12 June 2015, 19:55:29 UTC, committed by Iman Sarrafi on 12 June 2015, 19:55:29 UTC
1 parent 85704b9
Tip revision: f380a5b33b7e915f14b16e9c2fcda187d8753936 authored by Iman Sarrafi on 12 June 2015, 19:55:29 UTC
Updated README.md
Updated README.md
Tip revision: f380a5b
Makefile
MRSFAST_VERSION := "3.3.7"
BUILD_DATE := "$(shell date)"
all: OPTIMIZE_FLAGS build
debug: DEBUG_FLAGS build
profile: PROFILE_FLAGS build
build: clean_executables SSE_FLAGS mrsfast snp_indexer clean_objects
LDFLAGS=#-static
LIBS=-lz -lm -pthread -lpthread
CFLAGS=-fno-pic -DMRSFAST_VERSION=\"$(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
mrsfast: clean_executables $(objects)
ifeq ($(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: clean_executables SNPIndexer.o
gcc SNPIndexer.o -o $@ ${LDFLAGS} ${LIBS}
clean_objects: mrsfast snp_indexer
@rm -f $(objects)
@rm -f SNPIndexer.o
@rm -f HELPstub.c
@rm -f HELPstub.o
clean:
@rm -f $(objects)
@rm -f SNPIndexer.o
@rm -f HELPstub.c
@rm -f HELPstub.o
clean_executables:
@rm -f mrsfast
@rm -f snp_indexer
HELP.o:
@groff -Tascii -man ./HELP.man > HELP
ifeq ($(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
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