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|
#
# Makefile for bowtie, bowtie-build, bowtie-inspect
#
prefix = /usr/local
bindir = $(prefix)/bin
ARCH = $(shell uname -m)
INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) -I third_party
LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz -lpthread
HEADERS = $(wildcard *.h)
BOWTIE_MM = 1
BOWTIE_SHARED_MEM = 1
EXTRA_FLAGS =
EXTRA_CFLAGS =
EXTRA_CXXFLAGS = -std=c++03
CFLAGS += $(EXTRA_CFLAGS)
CXXFLAGS += $(EXTRA_CXXFLAGS)
WARNING_FLAGS = -Wall -Wno-unused-parameter -Wno-reorder
RELEASE_DEPENDENCIES = $(if $(RELEASE_BUILD),static-libs)
# Detect Cygwin or MinGW
WINDOWS =
CYGWIN =
MINGW =
ifneq (,$(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,$(shell uname)))
WINDOWS = 1
MINGW = 1
# POSIX memory-mapped files not currently supported on Windows
BOWTIE_MM = 0
BOWTIE_SHARED_MEM = 0
endif
endif
MACOS =
ifneq (,$(findstring Darwin,$(shell uname)))
MACOS = 1
ifneq (,$(findstring 13,$(shell uname -r)))
override EXTRA_FLAGS += -stdlib=libstdc++
endif
ifeq (1, $(RELEASE_BUILD))
EXTRA_FLAGS += -mmacosx-version-min=10.9
endif
endif
LINUX =
ifneq (,$(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,$(BOWTIE_SHARED_MEM))
SHMEM_DEF = -DBOWTIE_SHARED_MEM
endif
ifeq (1,$(MINGW))
override EXTRA_FLAGS += -static-libgcc -static-libstdc++
endif
POPCNT_CAPABILITY ?= 1
ifeq (,$(filter $(shell uname -m), x86_64))
POPCNT_CAPABILITY=0
endif
ifeq (1, $(POPCNT_CAPABILITY))
override EXTRA_FLAGS += -DPOPCNT_CAPABILITY
endif
PREFETCH_LOCALITY = 2
PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
SEARCH_LIBS =
BUILD_LIBS =
INSPECT_LIBS =
ifeq (1,$(MINGW))
BUILD_LIBS =
INSPECT_LIBS =
endif
ifeq (1,$(WITH_THREAD_PROFILING))
override EXTRA_FLAGS += -DPER_THREAD_TIMING=1
endif
OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
edit.cpp ebwt.cpp bt2_locks.cpp
ifeq (1,$(WITH_QUEUELOCK))
NO_SPINLOCK = 1
override EXTRA_FLAGS += -DWITH_QUEUELOCK
endif
ifeq (1,$(NO_SPINLOCK))
$(info $(NO_SPINLOCK))
override EXTRA_FLAGS += -DNO_SPINLOCK
endif
ifeq (1,$(WITH_FINE_TIMER))
override EXTRA_FLAGS += -DUSE_FINE_TIMER=1
endif
ifeq (1,$(WITH_COHORTLOCK))
override EXTRA_FLAGS += -DWITH_COHORTLOCK=1
OTHER_CPPS += cohort.cpp cpu_numa_info.cpp
endif
OTHER_CPPS += tinythread.cpp
SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp \
log.cpp hit_set.cpp sam.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 = $(shell cat VERSION)
BITS=32
ifeq (1,$(shell echo __LP64__ | $(CC) -P -E - | tr -d '\n'))
BITS=64
endif
# msys will always be 32 bit so look at the cpu arch instead.
ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
ifeq (1,$(MINGW))
BITS=64
endif
endif
ifeq (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)
DATE_FMT = %Y-%m-%dT%H:%M:%S
ifdef SOURCE_DATE_EPOCH
BUILD_DATE ?= $(shell date -u -d "@$(SOURCE_DATE_EPOCH)" "+$(DATE_FMT)" 2>/dev/null || date -u -r "$(SOURCE_DATE_EPOCH)" "+$(DATE_FMT)" 2>/dev/null || date -u "+$(DATE_FMT)")
BUILD_HOST := reproduciblebuild
else
BUILD_DATE ?= $(shell date "+$(DATE_FMT)")
BUILD_HOST ?= `hostname`
endif
DEFS=-fno-strict-aliasing \
-DBOWTIE_VERSION="\"`cat VERSION`\"" \
-DBUILD_HOST="\"Debian-reproducible\"" \
-DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" \
-DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" \
$(FILE_FLAGS) \
$(PTHREAD_DEF) \
$(PREF_DEF) \
$(MM_DEF) \
$(SHMEM_DEF)
ALL_FLAGS = $(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS)
DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(subst $(shell pwd),.,$(ALL_FLAGS))\""
RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(subst $(shell pwd),.,$(ALL_FLAGS))\""
#
# bowtie-build targets
#
bowtie-build-s: ebwt_build.cpp $(OTHER_CPPS) $(HEADERS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(ALL_FLAGS) \
$(DEFS) $(NOASSERT_FLAGS) $(WARNING_FLAGS) \
$(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) $(WARNING_FLAGS) \
$(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) $(WARNING_FLAGS) \
$(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) $(WARNING_FLAGS) \
$(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 $(WARNING_FLAGS) \
$(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) $(WARNING_FLAGS) \
$(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 $(WARNING_FLAGS) \
$(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) $(WARNING_FLAGS) \
$(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) $(WARNING_FLAGS) \
$(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 $(WARNING_FLAGS) \
$(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) $(WARNING_FLAGS) \
$(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 $(WARNING_FLAGS) \
$(INC) -I . \
-o $@ $< \
$(OTHER_CPPS) \
$(LIBS)
bowtie-inspect-s-debug: bowtie_inspect.cpp $(HEADERS) $(OTHER_CPPS)
$(CXX) $(DEBUG_FLAGS) \
$(DEBUG_DEFS) $(ALL_FLAGS) \
$(DEFS) $(WARNING_FLAGS) \
$(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 $(WARNING_FLAGS) \
$(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)-src
zip -r tmp.zip $(SRC_PKG_LIST)
mv tmp.zip .src.tmp/bowtie-$(VERSION)-src
cd .src.tmp/bowtie-$(VERSION)-src ; unzip tmp.zip ; rm -f tmp.zip
cd .src.tmp ; zip -r bowtie-$(VERSION)-src.zip bowtie-$(VERSION)-src
cp .src.tmp/bowtie-$(VERSION)-src.zip .
rm -rf .src.tmp
bowtie-bin.zip: $(RELEASE_DEPENDENCIES) $(BIN_PKG_LIST) $(BIN_LIST) $(BIN_LIST_AUX)
$(eval PKG_DIR=bowtie-$(VERSION)-$(if $(MACOS),macos,$(if $(MINGW),mingw,linux))-$(ARCH))
chmod a+x scripts/*.sh scripts/*.pl
rm -rf .bin.tmp
mkdir .bin.tmp
mkdir -p .bin.tmp/$(PKG_DIR)
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) $(BIN_LIST_AUX) ; \
fi
mv tmp.zip .bin.tmp/$(PKG_DIR)
cd .bin.tmp/$(PKG_DIR) ; unzip tmp.zip ; rm -f tmp.zip
cd .bin.tmp ; zip -r $(PKG_DIR).zip $(PKG_DIR)
cp .bin.tmp/$(PKG_DIR).zip .
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 -B .tmp.head \
--ascii \
--css style.css -o $@ \
--from markdown --to HTML \
--metadata title:"Bowtie Manual" \
--table-of-contents $^
MANUAL: MANUAL.markdown
perl doc/strip_markdown.pl < $^ > $@
.PHONY: install
install: all
mkdir -p $(DESTDIR)$(bindir)
for file in $(BIN_LIST) bowtie-inspect bowtie-build bowtie ; do \
cp -f $$file $(DESTDIR)$(bindir) ; \
done
.PHONY: simple-test
simple-test: all
./scripts/test/simple_tests.pl --bowtie=./bowtie --bowtie-build=./bowtie-build
.PHONY: random-test
random-test: all
eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
./scripts/test/random_bowtie_tests.sh $(*-command-variables-*-)
.PHONY: perl-deps
perl-deps:
if [ ! -e .perllib.tmp ]; then \
DL=$$([ `which wget` ] && echo "wget -O-" || echo "curl -L") ; \
mkdir .perllib.tmp ; \
$$DL http://cpanmin.us | perl - -l $(CURDIR)/.perllib.tmp App::cpanminus local::lib ; \
eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
cpanm --force Math::Random Clone Test::Deep Sys::Info -n --quiet; \
fi
static-libs:
if [ ! -d $(CURDIR)/.lib ]; then \
mkdir $(CURDIR)/.lib ; \
fi ; \
if [ ! -d $(CURDIR)/.include ]; then \
mkdir $(CURDIR)/.include ; \
fi ;
if [ `uname` == "Darwin" ]; then \
export CFLAGS=-mmacosx-version-min=10.9 ; \
export CXXFLAGS=-mmacosx-version-min=10.9 ; \
fi ; \
DL=$$([ `which wget` ] && echo "wget --no-check-certificate --content-disposition" || echo "curl -LJkO") ; \
cd /tmp ; \
$$DL https://zlib.net/zlib-1.2.11.tar.gz && tar xzf zlib-1.2.11.tar.gz && cd zlib-1.2.11 ; \
$(if $(MINGW), mingw32-make -f win32/Makefile.gcc, ./configure --static && make) && cp libz.a $(CURDIR)/.lib && cp zconf.h zlib.h $(CURDIR)/.include ;
.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
rm -f bowtie-align-s-master* bowtie-align-s-no-io*
rm -rf .lib .include
|
