Makefile

#
# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
#
# This file is part of Bowtie 2.
#
# Bowtie 2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Bowtie 2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Bowtie 2.  If not, see <http://www.gnu.org/licenses/>.
#

#
# Makefile for bowtie, bowtie2-build, bowtie2-inspect
#

PREFIX := /usr/local
bindir := $(PREFIX)/bin

LDLIBS := -lpthread -lz

HEADERS := $(wildcard *.h)
BOWTIE_MM := 1
BOWTIE_SHARED_MEM :=

CXXFLAGS += -std=c++11 -Wall -Wno-unused-but-set-variable

SRA_TOOLS_VER ?= 3.0.9
VDB_VER ?= 3.0.9

ifneq (,$(findstring $(shell uname),Linux))
  LDLIBS += -lrt
endif

# Detect Cygwin or MinGW
ifneq (,$(findstring mingw,$(shell $(CXX) --version)))
  WINDOWS := 1
  MINGW := 1
endif

ifeq (1, $(MINGW))
  LDLIBS := $(subst -lrt,,$(LDLIBS))
  CXX = x86_64-w64-mingw32-g++-posix
  CC  = x86_64-w64-mingw32-gcc-posix
  AR  = x86_64-w64-mingw32-ar
  RC  = x86_64-w64-mingw32-windres
  LD  = x86_64-w64-mingw32-ld
  STRIP = x86_64-w64-mingw32-strip
endif

# POSIX memory-mapped files not currently supported on Windows
ifeq (1, $(WINDOWS))
  BOWTIE_MM :=
  BOWTIE_SHARED_MEM :=
endif

MACOS :=
ifneq (,$(findstring Darwin,$(shell uname)))
  MACOS := 1
  ifeq (1,$(shell uname -r | awk -F. '{ if ($$1 > 12 && $$1 < 16) print 1; }'))
	CXXFLAGS += -stdlib=libstdc++
  endif
  ifdef STATIC_BUILD
	CXXFLAGS += -mmacosx-version-min=10.9
  endif
endif

BITS := 32
ARCH ?= $(shell uname -m)
ifneq (,$(findstring $(ARCH), x86_64 amd64))
  BITS := 64
  ifeq (1, $(SSE_AVX2))
	SSE_FLAG := -mavx2 -faligned-new -DSSE_AVX2
  else
	SSE_FLAG := -msse2
  endif

  POPCNT_CAPABILITY ?= 1
else ifneq (,$(findstring $(ARCH), aarch64 arm64 s390x powerpc64 powerpc64le ppc64 ppc64le))
  BITS := 64
  SSE_FLAG :=
  CXXFLAGS += -fopenmp-simd
  CPPFLAGS += -Ithird_party
  POPCNT_CAPABILITY ?= 0
endif

ifeq (1, $(if $(or $(USE_SAIS),$(USE_SAIS_OPENMP)),1))
  CPPFLAGS += -Ithird_party/libsais/include
ifdef USE_SAIS_OPENMP
  BUILD_CXXFLAGS += -fopenmp
endif
  BUILD_CXXFLAGS += -DUSE_SAIS
  BUILD_LDFLAGS += -Lthird_party/libsais/lib
  BUILD_LDLIBS += -lsais
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

ifdef STATIC_BUILD
  WITH_ZSTD = 1
  LDFLAGS += -L$(CURDIR)/.tmp/lib
  CPPFLAGS += -I$(CURDIR)/.tmp/include
endif

ifeq (1, $(POPCNT_CAPABILITY))
  CXXFLAGS += -DPOPCNT_CAPABILITY
  CPPFLAGS += -I third_party
endif

MM_DEF :=

ifeq (1,$(BOWTIE_MM))
  MM_DEF := -DBOWTIE_MM
endif

SHMEM_DEF :=

ifdef BOWTIE_SHARED_MEM
  SHMEM_DEF := -DBOWTIE_SHARED_MEM
endif

PTHREAD_PKG :=
PTHREAD_LIB :=

ifeq (1,$(MINGW))
  PTHREAD_LIB :=
else
  PTHREAD_LIB := -lpthread
endif

ifeq (1,$(NO_SPINLOCK))
  CXXFLAGS += -DNO_SPINLOCK
endif

USE_SRA ?=
ifeq (1, $(USE_SRA))
  ifdef MINGW
    $(error "SRA binaries cannot be built on MINGW")
  else
    LDFLAGS += -L$(CURDIR)/.tmp/lib64
    ifndef ($(STATIC_BUILD))
      CPPFLAGS += -I$(CURDIR)/.tmp/include
    endif
    ALIGN_LDLIBS += -lncbi-ngs-static
    ALIGN_LDLIBS += -lncbi-vdb-static
    ALIGN_LDLIBS += -ldl
    CXXFLAGS += -DUSE_SRA
  endif
endif

ifeq (1,$(WITH_THREAD_PROFILING))
  CXXFLAGS += -DPER_THREAD_TIMING=1
endif

ifeq (1,$(WITH_AFFINITY))
  CXXFLAGS += -DWITH_AFFINITY=1
endif

#default is to use queue lock for better thread scaling performance
ifneq (1,$(NO_QUEUELOCK))
  CXXFLAGS += -DNO_SPINLOCK
  CXXFLAGS += -DWITH_QUEUELOCK=1
endif

SHARED_CPPS :=  ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
  edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp \
  reference.cpp ds.cpp multikey_qsort.cpp limit.cpp \
  random_source.cpp

SEARCH_CPPS :=  qual.cpp pat.cpp sam.cpp \
  read_qseq.cpp aligner_seed_policy.cpp \
  aligner_seed.cpp \
  aligner_seed2.cpp \
  aligner_sw.cpp \
  aligner_sw_driver.cpp aligner_cache.cpp \
  aligner_result.cpp ref_coord.cpp mask.cpp \
  pe.cpp aln_sink.cpp dp_framer.cpp \
  scoring.cpp presets.cpp unique.cpp \
  simple_func.cpp \
  random_util.cpp \
  aligner_bt.cpp sse_util.cpp \
  aligner_swsse.cpp outq.cpp \
  aligner_swsse_loc_i16.cpp \
  aligner_swsse_ee_i16.cpp \
  aligner_swsse_loc_u8.cpp \
  aligner_swsse_ee_u8.cpp \
  aligner_driver.cpp

ifeq (1, $(WITH_ZSTD))
  LDLIBS += -lzstd
  CXXFLAGS += -DWITH_ZSTD
  SHARED_CPPS += zstd_decompress.cpp
endif

SEARCH_CPPS_MAIN := $(SEARCH_CPPS) bowtie_main.cpp

DP_CPPS := qual.cpp aligner_sw.cpp aligner_result.cpp ref_coord.cpp mask.cpp \
  simple_func.cpp sse_util.cpp aligner_bt.cpp aligner_swsse.cpp \
  aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp \
  aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp scoring.cpp

BUILD_CPPS := diff_sample.cpp
BUILD_CPPS_MAIN := $(BUILD_CPPS) bowtie_build_main.cpp

SEARCH_FRAGMENTS := $(wildcard search_*_phase*.c)
VERSION := $(shell cat BOWTIE2_VERSION)

SANITIZER_FLAGS :=
ifeq (0,$(shell $(CXX) -E -fsanitize=address,undefined btypes.h > /dev/null 2>&1; echo $$?))
  SANITIZER_FLAGS := -fsanitize=address,undefined
else ifeq (0,$(shell $(CXX) -E -fsanitize=address btypes.h > /dev/null 2>&1; echo $$?))
  SANITIZER_FLAGS := -fsanitize=address
else ifeq (0,$(shell $(CXX) -E -fsanitize=undefined btypes.h > /dev/null 2>&1; echo $$?))
  SANITIZER_FLAGS := -fsanitize=undefined
endif

DEBUG_FLAGS    := -O0 -g3 $(SSE_FLAG)
RELEASE_FLAGS  := -O3 $(SSE_FLAG) -funroll-loops -g3
NOASSERT_FLAGS := -DNDEBUG
FILE_FLAGS     := -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(CXXFLAGS)\""
RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(CXXFLAGS)\""

BOWTIE2_BIN_LIST := bowtie2-build-s \
  bowtie2-build-l \
  bowtie2-align-s \
  bowtie2-align-l \
  bowtie2-inspect-s \
  bowtie2-inspect-l
BOWTIE2_BIN_LIST_DBG := bowtie2-build-s-debug \
  bowtie2-build-l-debug \
  bowtie2-align-s-debug \
  bowtie2-align-l-debug \
  bowtie2-inspect-s-debug \
  bowtie2-inspect-l-debug
BOWTIE2_BIN_LIST_SAN := bowtie2-build-s-sanitized \
  bowtie2-build-l-sanitized \
  bowtie2-align-s-sanitized \
  bowtie2-align-l-sanitized \
  bowtie2-inspect-s-sanitized \
  bowtie2-inspect-l-sanitized
ifndef SANITIZER_FLAGS
        BOWTIE2_BIN_LIST_SAN =
endif

GENERAL_LIST := $(wildcard scripts/*.sh) \
  $(wildcard scripts/*.pl) \
  doc/manual.html \
  doc/README \
  doc/style.css \
  $(wildcard example/index/*.bt2) \
  $(wildcard example/reads/*.fq) \
  $(wildcard example/reads/*.pl) \
  example/reads/combined_reads.bam \
  example/reference/lambda_virus.fa \
  $(PTHREAD_PKG) \
  bowtie2 \
  bowtie2-build \
  bowtie2-inspect \
  AUTHORS \
  LICENSE \
  NEWS \
  MANUAL \
  MANUAL.markdown \
  README.md \
  TUTORIAL \
  BOWTIE2_VERSION

ifeq (1,$(WINDOWS))
  BOWTIE2_BIN_LIST := $(BOWTIE2_BIN_LIST) bowtie2.bat bowtie2-build.bat bowtie2-inspect.bat
  CXXFLAGS += -static-libgcc -static-libstdc++ -static
endif

# This is helpful on Windows under MinGW/MSYS, where Make might go for
# the Windows FIND tool instead.
FIND := $(shell which find)

SRC_PKG_LIST = $(wildcard *.h) \
  $(wildcard *.hh) \
  $(wildcard *.c) \
  $(wildcard *.cpp) \
  $(wildcard third_party/*) \
  Makefile \
  CMakeLists.txt \
  $(GENERAL_LIST)

ifeq (1,$(WINDOWS))
  BIN_PKG_LIST := $(GENERAL_LIST) bowtie2.bat bowtie2-build.bat bowtie2-inspect.bat
else
  BIN_PKG_LIST := $(GENERAL_LIST)
endif

.PHONY: all allall both both-debug

all: $(BOWTIE2_BIN_LIST) ;
allall: $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG) $(BOWTIE2_BIN_LIST_SAN) ;
both: bowtie2-align-s bowtie2-build-s bowtie2-align-l bowtie2-build-l ;
both-debug: bowtie2-align-s-debug bowtie2-build-s-debug bowtie2-align-l-debug bowtie2-build-l-debug ;
both-sanitized: bowtie2-align-s-sanitized bowtie2-build-s-sanitized bowtie2-align-l-sanitized bowtie2-build-l-sanitized ;

DEFS := -fno-strict-aliasing \
  -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" \
  -DBUILD_HOST="\"$${HOSTNAME:-`hostname`}\"" \
  -DBUILD_TIME="\"`date -u`\"" \
  -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
  $(FILE_FLAGS) \
  $(PREF_DEF) \
  $(MM_DEF) \
  $(SHMEM_DEF)

# set compiler flags for all sanitized builds
ifdef BOWTIE2_BIN_LIST_SAN
$(BOWTIE2_BIN_LIST_SAN): CXXFLAGS+=$(SANITIZER_FLAGS)
else
$(BOWTIE2_BIN_LIST_SAN): $(error "Compiler does not support...")
endif

bowtie2-build-%: CXXFLAGS += $(BUILD_CXXFLAGS)
bowtie2-build-%: LDFLAGS += $(BUILD_LDFLAGS)
bowtie2-build-%: LDLIBS += $(BUILD_LDLIBS)

bowtie2-align-%: LDLIBS += $(ALIGN_LDLIBS)
#
# bowtie2-build targets
#
bowtie2-build-s-sanitized bowtie2-build-s: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
		$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS)  \
		$(CPPFLAGS) \
		-o $@ $< \
		$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
		$(LDFLAGS) $(LDLIBS)

bowtie2-build-l-sanitized bowtie2-build-l: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
		$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS)  \
		$(CPPFLAGS) \
		-o $@ $< \
		$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
		$(LDFLAGS) $(LDLIBS)

bowtie2-build-s-debug: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
	$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(CXXFLAGS) \
		$(DEFS) -DBOWTIE2  \
		$(CPPFLAGS) \
		-o $@ $< \
		$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
		$(LDFLAGS) $(LDLIBS)

bowtie2-build-l-debug: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
	$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(CXXFLAGS) \
		$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX  \
		$(CPPFLAGS) \
		-o $@ $< \
		$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
		$(LDFLAGS) $(LDLIBS)

#
# bowtie2-align targets
#

bowtie2-align-s-sanitized bowtie2-align-s: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
		$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) \
		$(CPPFLAGS) \
		-o $@ $< \
		$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
		$(LDFLAGS) $(LDLIBS)

bowtie2-align-l-sanitized bowtie2-align-l: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
		$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS)  \
		$(CPPFLAGS) \
		-o $@ $< \
		$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
		$(LDFLAGS) $(LDLIBS)

bowtie2-align-s-debug: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
	$(CXX) $(DEBUG_FLAGS) \
		$(DEBUG_DEFS) $(CXXFLAGS) \
		$(DEFS) -DBOWTIE2  \
		$(CPPFLAGS) \
		-o $@ $< \
		$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
		$(LDFLAGS) $(LDLIBS)

bowtie2-align-l-debug: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
	$(CXX) $(DEBUG_FLAGS) \
		$(DEBUG_DEFS) $(CXXFLAGS) \
		$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX  \
		$(CPPFLAGS) \
		-o $@ $< \
		$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
		$(LDFLAGS) $(LDLIBS)

#
# bowtie2-inspect targets
#

bowtie2-inspect-s-sanitized bowtie2-inspect-s: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
	$(CXX) $(RELEASE_FLAGS) \
		$(RELEASE_DEFS) $(CXXFLAGS) \
		$(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN  \
		$(CPPFLAGS) \
		-o $@ $< \
		$(SHARED_CPPS) \
		$(LDFLAGS) $(LDLIBS)

bowtie2-inspect-l-sanitized bowtie2-inspect-l: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
	$(CXX) $(RELEASE_FLAGS) \
		$(RELEASE_DEFS) $(CXXFLAGS) \
		$(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN  -DBOWTIE_64BIT_INDEX  \
		$(CPPFLAGS) \
		-o $@ $< \
		$(SHARED_CPPS) \
		$(LDFLAGS) $(LDLIBS)

bowtie2-inspect-s-debug: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
	$(CXX) $(DEBUG_FLAGS) \
		$(DEBUG_DEFS) $(CXXFLAGS) \
		$(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN  \
		$(CPPFLAGS) \
		-o $@ $< \
		$(SHARED_CPPS) \
		$(LDFLAGS) $(LDLIBS)

bowtie2-inspect-l-debug: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
	$(CXX) $(DEBUG_FLAGS) \
		$(DEBUG_DEFS) $(CXXFLAGS) \
		$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DBOWTIE_INSPECT_MAIN  \
		$(CPPFLAGS) \
		-o $@ $< \
		$(SHARED_CPPS) \
		$(LDFLAGS) $(LDLIBS)

#
# bowtie2-dp targets
#

bowtie2-dp: bt2_dp.cpp $(HEADERS) $(SHARED_CPPS) $(DP_CPPS)
	$(CXX) $(RELEASE_FLAGS) \
		$(RELEASE_DEFS) $(CXXFLAGS) $(NOASSERT_FLAGS) \
		$(DEFS) -DBOWTIE2 -DBOWTIE_DP_MAIN  \
		$(CPPFLAGS) \
		-o $@ $< \
		$(DP_CPPS) $(SHARED_CPPS) \
		$(LDFLAGS) $(LDLIBS)

bowtie2-dp-debug: bt2_dp.cpp $(HEADERS) $(SHARED_CPPS) $(DP_CPPS)
	$(CXX) $(DEBUG_FLAGS) \
		$(DEBUG_DEFS) $(CXXFLAGS) \
		$(DEFS) -DBOWTIE2 -DBOWTIE_DP_MAIN  \
		$(CPPFLAGS) \
		-o $@ $< \
		$(DP_CPPS) $(SHARED_CPPS) \
		$(LDFLAGS) $(LDLIBS)

bowtie2.bat:
	echo "@echo off" > bowtie2.bat
	echo "perl %~dp0/bowtie2 %*" >> bowtie2.bat

bowtie2-build.bat:
	echo "@echo off" > bowtie2-build.bat
	echo "python3 %~dp0/bowtie2-build %*" >> bowtie2-build.bat

bowtie2-inspect.bat:
	echo "@echo off" > bowtie2-inspect.bat
	echo "python3 %~dp0/bowtie2-inspect %*" >> bowtie2-inspect.bat

.PHONY: bowtie2-src-pkg
bowtie2-src-pkg: $(SRC_PKG_LIST)
	chmod a+x scripts/*.sh scripts/*.pl
	mkdir .src.tmp
	mkdir .src.tmp/bowtie2-$(VERSION)
	zip tmp.zip $(SRC_PKG_LIST)
	mv tmp.zip .src.tmp/bowtie2-$(VERSION)
	cd .src.tmp/bowtie2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
	cd .src.tmp ; zip -r bowtie2-$(VERSION)-source.zip bowtie2-$(VERSION)
	cp .src.tmp/bowtie2-$(VERSION)-source.zip .
	rm -rf .src.tmp

.PHONY: bowtie2-bin-pkg
bowtie2-bin-pkg: PKG_DIR := bowtie2-$(VERSION)-$(if $(USE_SRA),sra-)$(if $(MACOS),macos,$(if $(MINGW),mingw,linux))-$(ARCH)
bowtie2-bin-pkg: $(BIN_PKG_LIST) $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG)
	chmod a+x scripts/*.sh scripts/*.pl
	rm -rf .bin.tmp
	mkdir -p .bin.tmp/$(PKG_DIR)
	if [ -f bowtie2-align-s.exe ] ; then \
		zip tmp.zip $(BIN_PKG_LIST) $(addsuffix .exe,$(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG)) ; \
	else \
		zip tmp.zip $(BIN_PKG_LIST) $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG) ; \
	fi
	mv tmp.zip .bin.tmp/$(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

bowtie2-seeds-debug: aligner_seed.cpp ccnt_lut.cpp alphabet.cpp aligner_seed.h bt2_idx.cpp bt2_io.cpp
	$(CXX) $(DEBUG_FLAGS) \
		$(DEBUG_DEFS) $(CXXFLAGS) \
		-DSCAN_MAIN \
		$(DEFS)  \
		$(CPPFLAGS) \
		-o $@ $< \
		aligner_seed.cpp bt2_idx.cpp ccnt_lut.cpp alphabet.cpp bt2_io.cpp \
		$(LDFLAGS) $(LDLIBS)

.PHONY: doc
doc: doc/manual.html MANUAL

doc/manual.html: MANUAL.markdown
	echo "<h1>Table of Contents</h1>" > .tmp.head
	pandoc -B .tmp.head \
	       --metadata title:"Bowtie 2 Manual"\
	       --css doc/style.css -o $@ \
	       --from markdown-smart \
	       --to HTML \
	       --table-of-contents $^
	rm -f .tmp.head

MANUAL: MANUAL.markdown
	pandoc -f markdown-smart -t plain $^ -o $@

.PHONY: install
install: all
	mkdir -p $(DESTDIR)$(bindir)
	for file in $(BOWTIE2_BIN_LIST) bowtie2-inspect bowtie2-build bowtie2 ; do \
		cp -f $$file $(DESTDIR)$(bindir) ; \
	done

.PHONY: simple-test
simple-test: perl-deps both both-debug both-sanitized
	eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
	sh ./scripts/test/simple_tests.sh

.PHONY: random-test
random-test: all perl-deps
	eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
	sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2)

.PHONY: perl-deps
perl-deps:
	if [ ! -d "$(CURDIR)/.tmp" ]; then \
		mkdir -p $(CURDIR)/.tmp/include $(CURDIR)/.tmp/lib ; \
	fi
	DL=$$( ( which wget >/dev/null 2>&1 && echo "wget --no-check-certificate -O-" ) || echo "curl -L") ; \
	$$DL http://cpanmin.us | perl - -l $(CURDIR)/.tmp App::cpanminus local::lib ; \
	eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
	$(CURDIR)/.tmp/bin/cpanm --force File::Which Math::Random Clone Test::Deep Sys::Info ; \

.PHONY: static-libs
static-libs:
	if [ ! -d "$(CURDIR)/.tmp" ] ; then \
		mkdir -p $(CURDIR)/.tmp/include $(CURDIR)/.tmp/lib ; \
	fi ; \
	if [ `uname` = "Darwin" ]; then \
		export CFLAGS=-mmacosx-version-min=10.9 ; \
		export CXXFLAGS=-mmacosx-version-min=10.9 ; \
	fi ; \
	cd $(CURDIR)/.tmp ; \
	DL=$$( ( which wget >/dev/null 2>&1 && echo "wget --no-check-certificate" ) || echo "curl -LOk") ; \
	if [ ! -f "$(CURDIR)/.tmp/lib/libz.a" ] ; then \
		$$DL http://zlib.net/zlib-1.3.tar.gz && tar xzf zlib-1.3.tar.gz && cd zlib-1.3 ; \
		$(if $(MINGW), $(MAKE) libz.a -f win32/Makefile.gcc CC=$(CC) AR=$(AR) RC=$(RC) STRIP=$(STRIP) LD=$(LD), ./configure --static && make) && \
		cp zlib.h zconf.h $(CURDIR)/.tmp/include && cp libz.a $(CURDIR)/.tmp/lib ; \
		rm -rf zlib-1.3* ; \
	fi ; \
        if [ ! -f "$(CURDIR)/.tmp/lib/libzstd.a" ]; then \
                cd $(CURDIR)/.tmp ; \
                $$DL https://github.com/facebook/zstd/releases/download/v1.5.5/zstd-1.5.5.tar.gz && tar xzf zstd-1.5.5.tar.gz ; \
                cd zstd-1.5.5 && $(MAKE) CC=$(CC) AR=$(AR) RC=$(RC) STRIP=$(STRIP) LD=$(LD) lib ; \
                cd $(CURDIR)/.tmp/zstd-1.5.5/lib && cp zstd.h $(CURDIR)/.tmp/include && cp libzstd.a $(CURDIR)/.tmp/lib ; \
		rm -rf zstd-1.5.5* ; \
        fi

.PHONY: libsais
libsais:
	if [ ! -d $(CURDIR)/third_party/libsais ]; then \
		git submodule init && git submodule update --recursive ; \
	fi ; \
	if [ -n "$(USE_SAIS_OPENMP)" ]; then \
		export CFLAGS="$(CFLAGS) -fopenmp -O2" ; \
	fi ; \
	cd $(CURDIR)/third_party/libsais && $(MAKE) -B CC=$(CC) && $(MAKE) install PREFIX=$$PWD ;

.PHONY: sra-deps
sra-deps:
	DL=$$( ( which wget >/dev/null 2>&1 && echo "wget --no-check-certificate" ) || echo "curl -LOk") ; \
	if [ ! -d "$(CURDIR)/.tmp" ] ; then \
		mkdir -p $(CURDIR)/.tmp/include $(CURDIR)/.tmp/lib ; \
	fi ; \
	if [ `uname` = "Darwin" ]; then \
		export CFLAGS=-mmacosx-version-min=10.9 ; \
		export CXXFLAGS=-mmacosx-version-min=10.9 ; \
	fi ; \
	if [ ! -f "$(CURDIR)/.tmp/include/ncbi-vdb/NGS.hpp" ] ; then \
		if [ ! -d "$(CURDIR)/.tmp/ncbi-vdb-$(VDB_VER)/vdb3" ] ; then \
	 		cd $(CURDIR)/.tmp ; \
	 		$$DL https://github.com/ncbi/ncbi-vdb/archive/refs/tags/$(VDB_VER).tar.gz ; \
	  		tar zxvf $(VDB_VER).tar.gz ; \
	  		rm -f $(VDB_VER).tar.gz ; \
	  	fi ; \
	  	cd $(CURDIR)/.tmp/ncbi-vdb-$(VDB_VER) \
	 		&& ./configure --prefix=$(CURDIR)/.tmp --build-prefix=`pwd`/build --without-debug \
	 		&& make && make install ; \
	fi ; \
	if [ ! -f "$(CURDIR)/.tmp/include/ngs/Alignment.hpp" ] ; then \
		if [ ! -d "$(CURDIR)/.tmp/sra-tools-$(SRA_TOOLS_VER)" ] ; then \
			cd $(CURDIR)/.tmp ; \
			$$DL https://github.com/ncbi/sra-tools/archive/$(SRA_TOOLS_VER).tar.gz ; \
			tar xzvf $(SRA_TOOLS_VER).tar.gz ; \
			rm -f $(SRA_TOOLS_VER).tar.gz ; \
		fi ; \
		cd $(CURDIR)/.tmp/sra-tools-$(SRA_TOOLS_VER) \
			&& ./configure --prefix=$(CURDIR)/.tmp --build-prefix=`pwd`/build \
				--with-ncbi-vdb-prefix="$(CURDIR)/.tmp" --enable-static --without-debug \
			&& make && make install ; \
	fi ;

.PHONY: test
test: simple-test random-test

.PHONY: clean
clean:
	rm -f $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG) $(BOWTIE2_BIN_LIST_SAN) \
	$(addsuffix .exe,$(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG)) \
	bowtie2-*.zip
	rm -f core.* .tmp.head
	rm -rf *.dSYM
	rm -rf .tmp