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#
# Copyright 2011, Ben Langmead <blangmea@jhsph.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
#
INC =
GCC_PREFIX = $(shell dirname `which gcc`)
GCC_SUFFIX =
CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
CXX = $(CPP)
HEADERS = $(wildcard *.h)
BOWTIE_PTHREADS = 1
BOWTIE_MM = 1
BOWTIE_SHARED_MEM = 0
# Detect Cygwin or MinGW
WINDOWS = 0
ifneq (,$(findstring CYGWIN,$(shell uname)))
WINDOWS = 1
# POSIX memory-mapped files not currently supported on Windows
BOWTIE_MM = 0
BOWTIE_SHARED_MEM = 0
else
ifneq (,$(findstring MINGW,$(shell uname)))
WINDOWS = 1
# POSIX memory-mapped files not currently supported on Windows
BOWTIE_MM = 0
BOWTIE_SHARED_MEM = 0
endif
endif
MACOS = 0
ifneq (,$(findstring Darwin,$(shell uname)))
MACOS = 1
endif
MM_DEF =
ifeq (1,$(BOWTIE_MM))
MM_DEF = -DBOWTIE_MM
endif
SHMEM_DEF =
ifeq (1,$(BOWTIE_SHARED_MEM))
SHMEM_DEF = -DBOWTIE_SHARED_MEM
endif
PTHREAD_PKG =
PTHREAD_LIB =
PTHREAD_DEF =
ifeq (1,$(BOWTIE_PTHREADS))
PTHREAD_DEF = -DBOWTIE_PTHREADS
ifeq (1,$(WINDOWS))
# pthreads for windows forces us to be specific about the library
PTHREAD_LIB = -lpthreadGC2
PTHREAD_PKG = pthreadGC2.dll
else
# There's also -pthread, but that only seems to work on Linux
PTHREAD_LIB = -lpthread
endif
endif
PREFETCH_LOCALITY = 2
PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
LIBS =
SEARCH_LIBS = $(PTHREAD_LIB)
BUILD_LIBS =
SHARED_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
edit.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 \
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
SEARCH_CPPS_MAIN = $(SEARCH_CPPS) bowtie_main.cpp
BUILD_CPPS = diff_sample.cpp
BUILD_CPPS_MAIN = $(BUILD_CPPS) bowtie_build_main.cpp
SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
VERSION = $(shell cat VERSION)
EXTRA_FLAGS =
# Convert BITS=?? to a -m flag
BITS=32
ifeq (x86_64,$(shell uname -m))
BITS=64
endif
BITS_FLAG =
ifeq (32,$(BITS))
BITS_FLAG = -m32
endif
ifeq (64,$(BITS))
BITS_FLAG = -m64
endif
SSE_FLAG=-msse2
DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
RELEASE_FLAGS = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
NOASSERT_FLAGS = -DNDEBUG
FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
BOWTIE2_BIN_LIST = bowtie2-build \
bowtie2-align \
bowtie2-inspect
BOWTIE2_BIN_LIST_AUX = bowtie2-build-debug \
bowtie2-align-debug \
bowtie2-inspect-debug
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/reference/lambda_virus.fa \
$(PTHREAD_PKG) \
bowtie2 \
AUTHORS \
COPYING \
NEWS \
MANUAL \
MANUAL.markdown \
TUTORIAL \
VERSION
# This is helpful on Windows under MinGW/MSYS, where Make might go for
# the Windows FIND tool instead.
FIND=$(shell which find)
SRC_PKG_LIST = $(wildcard *.h) \
$(wildcard *.hh) \
$(wildcard *.c) \
$(wildcard *.cpp) \
doc/strip_markdown.pl \
Makefile \
$(GENERAL_LIST)
BIN_PKG_LIST = $(GENERAL_LIST)
.PHONY: all allall both both-debug
all: $(BOWTIE2_BIN_LIST)
allall: $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_AUX)
both: bowtie2 bowtie2-build
both-debug: bowtie2-align-debug bowtie2-build-debug
DEFS=-fno-strict-aliasing \
-DBOWTIE2_VERSION="\"`cat VERSION`\"" \
-DBUILD_HOST="\"`hostname`\"" \
-DBUILD_TIME="\"`date`\"" \
-DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
$(FILE_FLAGS) \
$(PTHREAD_DEF) \
$(PREF_DEF) \
$(MM_DEF) \
$(SHMEM_DEF)
#
# bowtie2-build targets
#
bowtie2-build: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
$(LIBS) $(BUILD_LIBS)
bowtie2-build-debug: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
$(DEFS) -DBOWTIE2 -Wall \
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
$(LIBS) $(BUILD_LIBS)
#
# bowtie targets
#
bowtie2-align: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
$(LIBS) $(SEARCH_LIBS)
bowtie2-align-debug: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(DEBUG_FLAGS) \
$(DEBUG_DEFS) $(EXTRA_FLAGS) \
$(DEFS) -DBOWTIE2 -Wall \
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
$(LIBS) $(SEARCH_LIBS)
#
# bowtie2-inspect targets
#
bowtie2-inspect: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
$(CXX) $(RELEASE_FLAGS) \
$(RELEASE_DEFS) $(EXTRA_FLAGS) \
$(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
$(LIBS)
bowtie2-inspect-debug: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
$(CXX) $(DEBUG_FLAGS) \
$(DEBUG_DEFS) $(EXTRA_FLAGS) \
$(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
$(LIBS)
.PHONY: bowtie2-src
bowtie2-src: $(SRC_PKG_LIST)
chmod a+x scripts/*.sh scripts/*.pl
mkdir .src.tmp
mkdir .src.tmp/bowtie2-$(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
bowtie2-bin: $(BIN_PKG_LIST) $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_AUX)
chmod a+x scripts/*.sh scripts/*.pl
rm -rf .bin.tmp
mkdir .bin.tmp
mkdir .bin.tmp/bowtie2-$(VERSION)
if [ -f bowtie.exe ] ; then \
zip tmp.zip $(BIN_PKG_LIST) $(addsuffix .exe,$(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_AUX)) ; \
else \
zip tmp.zip $(BIN_PKG_LIST) $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_AUX) ; \
fi
mv tmp.zip .bin.tmp/bowtie2-$(VERSION)
cd .bin.tmp/bowtie2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
cd .bin.tmp ; zip -r bowtie2-$(VERSION)-$(BITS).zip bowtie2-$(VERSION)
cp .bin.tmp/bowtie2-$(VERSION)-$(BITS).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) $(EXTRA_FLAGS) \
-DSCAN_MAIN \
$(DEFS) -Wall \
$(INC) -I . \
-o $@ $< \
aligner_seed.cpp bt2_idx.cpp ccnt_lut.cpp alphabet.cpp bt2_io.cpp \
$(LIBS)
.PHONY: doc
doc: doc/manual.html MANUAL
doc/manual.html: MANUAL.markdown
echo "<h1>Table of Contents</h1>" > .tmp.head
pandoc -T "Bowtie 2 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 $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_AUX) \
$(addsuffix .exe,$(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_AUX)) \
bowtie2-src.zip bowtie2-bin.zip
rm -f core.* .tmp.head
rm -rf *.dSYM
|
