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|
#
# Makefile for bowtie, bowtie-build, bowtie-inspect
#
SEQAN_DIR = /usr/include/seqan
SEQAN_INC = -I $(SEQAN_DIR)
INC = $(SEQAN_INC) -I third_party
CPP = g++
CXX = $(CPP)
CC = gcc
HEADERS = $(wildcard *.h)
BOWTIE_MM = 1
BOWTIE_SHARED_MEM = 1
EXTRA_FLAGS =
EXTRA_CFLAGS =
EXTRA_CXXFLAGS =
CFLAGS += $(EXTRA_CFLAGS)
CXXFLAGS += $(EXTRA_CXXFLAGS)
# Detect Cygwin or MinGW
WINDOWS = 0
CYGWIN = 0
MINGW = 0
ifneq (,$(findstring CYGWIN,$(shell uname)))
WINDOWS = 1
CYGWIN = 1
# POSIX memory-mapped files not currently supported on Windows
BOWTIE_MM = 0
BOWTIE_SHARED_MEM = 0
else
ifneq (,$(findstring MINGW,$(shell uname)))
WINDOWS = 1
MINGW = 1
# POSIX memory-mapped files not currently supported on Windows
BOWTIE_MM = 0
BOWTIE_SHARED_MEM = 0
endif
endif
MACOS = 0
ifneq (,$(findstring Darwin,$(shell uname)))
MACOS = 1
endif
ifneq (,$(findstring 13,$(shell uname -r)))
CPP = clang++
CC = clang
EXTRA_FLAGS += -stdlib=libstdc++
endif
LINUX = 0
ifneq (,$(findstring Linux,$(shell uname)))
LINUX = 1
ifeq (,$(findstring mips,$(shell uname -m)))
EXTRA_FLAGS += -Wl,--hash-style=both
endif
endif
MM_DEF =
ifeq (1,$(BOWTIE_MM))
MM_DEF = -DBOWTIE_MM
endif
SHMEM_DEF =
ifeq (1,$(BOWTIE_SHARED_MEM))
SHMEM_DEF = -DBOWTIE_SHARED_MEM
endif
PTHREAD_PKG =
PTHREAD_LIB =
PTHREAD_DEF =
ifeq (1,$(MINGW))
PTHREAD_LIB =
EXTRA_FLAGS += -static-libgcc -static-libstdc++
else
PTHREAD_LIB = -lpthread
endif
POPCNT_CAPABILITY ?= 1
ifeq (1, $(POPCNT_CAPABILITY))
EXTRA_FLAGS += -DPOPCNT_CAPABILITY
INC += -I third_party
endif
PREFETCH_LOCALITY = 2
PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
LIBS = $(PTHREAD_LIB)
SEARCH_LIBS =
BUILD_LIBS =
INSPECT_LIBS =
ifeq (1,$(MINGW))
BUILD_LIBS =
INSPECT_LIBS =
endif
OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
edit.cpp ebwt.cpp tinythread.cpp
SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp \
log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp \
color.cpp color_dec.cpp hit.cpp
SEARCH_CPPS_MAIN = $(SEARCH_CPPS) bowtie_main.cpp
BUILD_CPPS =
BUILD_CPPS_MAIN = $(BUILD_CPPS) bowtie_build_main.cpp
SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
VERSION = $(shell cat VERSION)
BITS=32
ifeq (x86_64,$(shell uname -m))
BITS=64
endif
# msys will always be 32 bit so look at the cpu arch instead.
ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
ifeq (1,$(MINGW))
BITS=64
endif
endif
ifeq (1,$(LINUX))
ifeq (x86_64, $(shell uname -p))
BITS=64
endif
endif
ifeq (32,$(BITS))
$(error bowtie2 compilation requires a 64-bit platform )
endif
DEBUG_FLAGS = -O0 -g3
RELEASE_FLAGS = -O3
NOASSERT_FLAGS = -DNDEBUG
FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
BIN_LIST = bowtie-build-s \
bowtie-build-l \
bowtie-align-s \
bowtie-align-l \
bowtie-inspect-s \
bowtie-inspect-l
BIN_LIST_AUX = bowtie-build-s-debug \
bowtie-build-l-debug \
bowtie-align-s-debug \
bowtie-align-l-debug \
bowtie-inspect-s-debug \
bowtie-inspect-l-debug
GENERAL_LIST = $(wildcard scripts/*.sh) \
$(wildcard scripts/*.pl) \
$(wildcard scripts/*.py) \
$(wildcard indexes/e_coli*) \
$(wildcard genomes/NC_008253.fna) \
$(wildcard reads/e_coli_1000.*) \
$(wildcard reads/e_coli_1000_*) \
bowtie \
bowtie-build \
bowtie-inspect \
doc/manual.html \
doc/README \
doc/style.css \
reads/e_coli_10000snp.fa \
reads/e_coli_10000snp.fq \
$(PTHREAD_PKG) \
AUTHORS \
LICENSE \
NEWS \
MANUAL \
MANUAL.markdown \
TUTORIAL \
VERSION
SRC_PKG_LIST = $(wildcard *.h) \
$(wildcard *.hh) \
$(wildcard *.c) \
$(wildcard *.cpp) \
$(wildcard third_party/*.h) \
$(wildcard third_party/*.hh) \
$(wildcard third_party/*.c) \
$(wildcard third_party/*.cpp) \
doc/strip_markdown.pl \
Makefile \
$(GENERAL_LIST)
BIN_PKG_LIST = $(GENERAL_LIST)
all: $(BIN_LIST)
allall: $(BIN_LIST) $(BIN_LIST_AUX)
DEFS=-fno-strict-aliasing \
-DBOWTIE_VERSION="\"`cat VERSION`\"" \
-DBUILD_HOST="\"`hostname`\"" \
-DBUILD_TIME="\"`date`\"" \
-DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
$(FILE_FLAGS) \
$(PTHREAD_DEF) \
$(PREF_DEF) \
$(MM_DEF) \
$(SHMEM_DEF)
ALL_FLAGS = $(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS)
DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\""
RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\""
#
# bowtie-build targets
#
bowtie-build-s: ebwt_build.cpp $(OTHER_CPPS) $(HEADERS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(ALL_FLAGS) \
$(DEFS) $(NOASSERT_FLAGS) -Wall \
$(INC) \
-o $@ $< \
$(OTHER_CPPS) $(BUILD_CPPS_MAIN) \
$(LIBS) $(BUILD_LIBS)
bowtie-build-l: ebwt_build.cpp $(OTHER_CPPS) $(HEADERS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(ALL_FLAGS) \
$(DEFS) -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \
$(INC) \
-o $@ $< \
$(OTHER_CPPS) $(BUILD_CPPS_MAIN) \
$(LIBS) $(BUILD_LIBS)
bowtie-build_prof: ebwt_build.cpp $(OTHER_CPPS) $(HEADERS)
$(CXX) $(RELEASE_FLAGS) -pg -p -g3 $(RELEASE_DEFS) $(ALL_FLAGS) \
$(DEFS) $(NOASSERT_FLAGS) -Wall \
$(INC) \
-o $@ $< \
$(OTHER_CPPS) $(BUILD_CPPS_MAIN) \
$(LIBS) $(BUILD_LIBS)
bowtie-build-s-debug: ebwt_build.cpp $(OTHER_CPPS) $(HEADERS)
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(ALL_FLAGS) \
$(DEFS) -Wall \
$(INC) \
-o $@ $< \
$(OTHER_CPPS) $(BUILD_CPPS_MAIN) \
$(LIBS) $(BUILD_LIBS)
bowtie-build-l-debug: ebwt_build.cpp $(OTHER_CPPS) $(HEADERS)
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(ALL_FLAGS) \
$(DEFS) -DBOWTIE_64BIT_INDEX -Wall \
$(INC) \
-o $@ $< \
$(OTHER_CPPS) $(BUILD_CPPS_MAIN) \
$(LIBS) $(BUILD_LIBS)
#
# bowtie targets
#
bowtie-align-s: ebwt_search.cpp $(SEARCH_CPPS) $(OTHER_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(ALL_FLAGS) \
$(DEFS) $(NOASSERT_FLAGS) -Wall \
$(INC) \
-o $@ $< \
$(OTHER_CPPS) $(SEARCH_CPPS_MAIN) \
$(LIBS) $(SEARCH_LIBS)
bowtie-align-l: ebwt_search.cpp $(SEARCH_CPPS) $(OTHER_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(ALL_FLAGS) \
$(DEFS) $(NOASSERT_FLAGS) -DBOWTIE_64BIT_INDEX -Wall \
$(INC) \
-o $@ $< \
$(OTHER_CPPS) $(SEARCH_CPPS_MAIN) \
$(LIBS) $(SEARCH_LIBS)
bowtie_prof: ebwt_search.cpp $(SEARCH_CPPS) $(OTHER_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(RELEASE_FLAGS) \
$(RELEASE_DEFS) -pg -p -g3 $(ALL_FLAGS) \
$(DEFS) $(NOASSERT_FLAGS) -Wall \
$(INC) \
-o $@ $< \
$(OTHER_CPPS) $(SEARCH_CPPS_MAIN) \
$(LIBS) $(SEARCH_LIBS)
bowtie-align-s-debug: ebwt_search.cpp $(SEARCH_CPPS) $(OTHER_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(DEBUG_FLAGS) \
$(DEBUG_DEFS) $(ALL_FLAGS) \
$(DEFS) -Wall \
$(INC) \
-o $@ $< \
$(OTHER_CPPS) $(SEARCH_CPPS_MAIN) \
$(LIBS) $(SEARCH_LIBS)
bowtie-align-l-debug: ebwt_search.cpp $(SEARCH_CPPS) $(OTHER_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(DEBUG_FLAGS) \
$(DEBUG_DEFS) $(ALL_FLAGS) \
$(DEFS) -DBOWTIE_64BIT_INDEX -Wall \
$(INC) \
-o $@ $< \
$(OTHER_CPPS) $(SEARCH_CPPS_MAIN) \
$(LIBS) $(SEARCH_LIBS)
#
# bowtie-inspect targets
#
bowtie-inspect-s: bowtie_inspect.cpp $(HEADERS) $(OTHER_CPPS)
$(CXX) $(RELEASE_FLAGS) \
$(RELEASE_DEFS) $(ALL_FLAGS) \
$(DEFS) -Wall \
$(INC) -I . \
-o $@ $< \
$(OTHER_CPPS) \
$(LIBS)
bowtie-inspect-l: bowtie_inspect.cpp $(HEADERS) $(OTHER_CPPS)
$(CXX) $(RELEASE_FLAGS) \
$(RELEASE_DEFS) $(ALL_FLAGS) \
$(DEFS) -DBOWTIE_64BIT_INDEX -Wall \
$(INC) -I . \
-o $@ $< \
$(OTHER_CPPS) \
$(LIBS)
bowtie-inspect-s-debug: bowtie_inspect.cpp $(HEADERS) $(OTHER_CPPS)
$(CXX) $(DEBUG_FLAGS) \
$(DEBUG_DEFS) $(ALL_FLAGS) \
$(DEFS) -Wall \
$(INC) -I . \
-o $@ $< \
$(OTHER_CPPS) \
$(LIBS)
bowtie-inspect-l-debug: bowtie_inspect.cpp $(HEADERS) $(OTHER_CPPS)
$(CXX) $(DEBUG_FLAGS) \
$(DEBUG_DEFS) $(ALL_FLAGS) \
$(DEFS) -DBOWTIE_64BIT_INDEX -Wall \
$(INC) -I . \
-o $@ $< \
$(OTHER_CPPS) \
$(LIBS)
bowtie-src.zip: $(SRC_PKG_LIST)
chmod a+x scripts/*.sh scripts/*.pl
mkdir .src.tmp
mkdir .src.tmp/bowtie-$(VERSION)
zip -r tmp.zip $(SRC_PKG_LIST)
mv tmp.zip .src.tmp/bowtie-$(VERSION)
cd .src.tmp/bowtie-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
cd .src.tmp ; zip -r $@ bowtie-$(VERSION)
cp .src.tmp/$@ .
rm -rf .src.tmp
bowtie-bin.zip: $(BIN_PKG_LIST) $(BIN_LIST) $(BIN_LIST_AUX)
chmod a+x scripts/*.sh scripts/*.pl
rm -rf .bin.tmp
mkdir .bin.tmp
mkdir .bin.tmp/bowtie-$(VERSION)
if [ -f bowtie-align-s.exe ] ; then \
zip tmp.zip $(BIN_PKG_LIST) $(addsuffix .exe,$(BIN_LIST) $(BIN_LIST_AUX)) ; \
else \
zip tmp.zip $(BIN_PKG_LIST) $(BIN_LIST) $(BIN_LIST_AUX) ; \
fi
mv tmp.zip .bin.tmp/bowtie-$(VERSION)
cd .bin.tmp/bowtie-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
cd .bin.tmp ; zip -r $@ bowtie-$(VERSION)
cp .bin.tmp/$@ .
rm -rf .bin.tmp
.PHONY: doc
doc: doc/manual.html MANUAL
doc/manual.html: MANUAL.markdown
echo "<h1>Table of Contents</h1>" > .tmp.head
pandoc -T "Bowtie Manual" -B .tmp.head \
--css style.css -o $@ \
--from markdown --to HTML \
--table-of-contents $^
MANUAL: MANUAL.markdown
perl doc/strip_markdown.pl < $^ > $@
.PHONY: clean
clean:
rm -f $(BIN_LIST) $(BIN_LIST_AUX) \
bowtie_prof \
$(addsuffix .exe,$(BIN_LIST) $(BIN_LIST_AUX) bowtie_prof) \
bowtie-src.zip bowtie-bin.zip
rm -f core.*
|
