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| # | |
| # Makefile for bowtie, bowtie-build, bowtie-inspect | |
| # | |
| prefix = /usr/local | |
| bindir = $(prefix)/bin | |
| SEQAN_DIR = SeqAn-1.1 | |
| SEQAN_INC = -I $(SEQAN_DIR) | |
| INC = $(SEQAN_INC) -I third_party | |
| CPP = g++ -w | |
| CXX = $(CPP) | |
| CC = gcc | |
| LIBS = $(LDFLAGS) -lz | |
| 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,$(shell uname))) | |
| MACOS = 1 | |
| ifneq (,$(findstring 13,$(shell uname -r))) | |
| CPP = clang++ | |
| CC = clang | |
| override EXTRA_FLAGS += -stdlib=libstdc++ | |
| endif | |
| ifneq (,$(findstring 14,$(shell uname -r))) | |
| CPP = clang++ | |
| CC = clang | |
| override EXTRA_FLAGS += -stdlib=libstdc++ | |
| endif | |
| endif | |
| LINUX = 0 | |
| ifneq (,$(findstring Linux,$(shell uname))) | |
| LINUX = 1 | |
| override EXTRA_FLAGS += -Wl,--hash-style=both | |
| endif | |
| MM_DEF = | |
| ifeq (1,$(BOWTIE_MM)) | |
| MM_DEF = -DBOWTIE_MM | |
| endif | |
| SHMEM_DEF = | |
| ifeq (1,$(BOWTIE_SHARED_MEM)) | |
| SHMEM_DEF = -DBOWTIE_SHARED_MEM | |
| endif | |
| PTHREAD_PKG = | |
| PTHREAD_LIB = | |
| PTHREAD_DEF = | |
| #if we're not using TBB, then we can't use queuing locks | |
| ifeq (1,$(NO_TBB)) | |
| NO_QUEUELOCK=1 | |
| endif | |
| ifeq (1,$(MINGW)) | |
| PTHREAD_LIB = | |
| override EXTRA_FLAGS += -static-libgcc -static-libstdc++ | |
| else | |
| PTHREAD_LIB = -lpthread | |
| endif | |
| ifeq (1,$(NO_SPINLOCK)) | |
| override EXTRA_FLAGS += -DNO_SPINLOCK | |
| endif | |
| ifneq (1,$(NO_TBB)) | |
| LIBS += $(PTHREAD_LIB) -ltbb | |
| ifeq (1, $(RELEASE_BIN)) | |
| LIBS += -ltbbmalloc | |
| else | |
| LIBS += -ltbbmalloc_proxy | |
| endif | |
| override EXTRA_FLAGS += -DWITH_TBB | |
| else | |
| LIBS += $(PTHREAD_LIB) | |
| endif | |
| POPCNT_CAPABILITY ?= 1 | |
| ifeq (1, $(POPCNT_CAPABILITY)) | |
| override EXTRA_FLAGS += -DPOPCNT_CAPABILITY | |
| INC += -I third_party | |
| endif | |
| PREFETCH_LOCALITY = 2 | |
| PREF_DEF = -DPREFETCH_LOCALITY=$(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 | |
| ifeq (1,$(WITH_AFFINITY)) | |
| override EXTRA_FLAGS += -DWITH_AFFINITY=1 | |
| endif | |
| ifeq (1,$(WITH_QUEUELOCK)) | |
| override EXTRA_FLAGS += -DWITH_QUEUELOCK=1 | |
| endif | |
| ifeq (1,$(WITH_FINE_TIMER)) | |
| override EXTRA_FLAGS += -DUSE_FINE_TIMER=1 | |
| endif | |
| OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \ | |
| edit.cpp ebwt.cpp | |
| ifeq (1,$(WITH_COHORTLOCK)) | |
| override EXTRA_FLAGS += -DWITH_COHORTLOCK=1 | |
| OTHER_CPPS += cohort.cpp cpu_numa_info.cpp | |
| endif | |
| ifeq (1,$(NO_TBB)) | |
| OTHER_CPPS += tinythread.cpp | |
| endif | |
| 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 -m64 | |
| RELEASE_FLAGS = -O3 -m64 | |
| 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_*) \ | |
| SeqAn-1.1 \ | |
| 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) $(CFLAGS) $(CXXFLAGS) | |
| DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(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: install | |
| install: all | |
| mkdir -p $(DESTDIR)$(bindir) | |
| for file in $(BIN_LIST) bowtie-inspect bowtie-build bowtie ; do \ | |
| cp -f $$file $(DESTDIR)$(bindir) ; \ | |
| done | |
| .PHONY: simple-test | |
| simple-test: allall perl-deps | |
| eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \ | |
| ./scripts/test/simple_tests.pl --bowtie=./bowtie --bowtie-build=./bowtie-build | |
| .PHONY: random-test | |
| random-test: all perl-deps | |
| eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \ | |
| ./scripts/test/random_bowtie_tests.sh | |
| .PHONY: perl-deps | |
| perl-deps: | |
| if [ ! -e .perllib.tmp ]; then \ | |
| DL=$$([ `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 | |
| .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* |