#
# Copyright 2014, Daehwan Kim <infphilo@gmail.com>
#
# This file is part of Centrifuge, which is copied and modified from Makefile in the Bowtie2 package.
#
# Centrifuge 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.
#
# Centrifuge 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 Centrifuge. If not, see <http://www.gnu.org/licenses/>.
#
#
# Makefile for centrifuge-bin, centrifuge-build, centrifuge-inspect
#
INC =
GCC_PREFIX = $(shell dirname `which gcc`)
GCC_SUFFIX =
CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
CXX = $(CPP) #-fdiagnostics-color=always
HEADERS = $(wildcard *.h)
BOWTIE_MM = 1
BOWTIE_SHARED_MEM = 0
# Detect Cygwin or MinGW
WINDOWS = 0
CYGWIN = 0
MINGW = 0
ifneq (,$(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
POPCNT_CAPABILITY ?= 1
ifeq (1, $(POPCNT_CAPABILITY))
EXTRA_FLAGS += -DPOPCNT_CAPABILITY
INC += -I third_party
endif
MM_DEF =
ifeq (1,$(BOWTIE_MM))
MM_DEF = -DBOWTIE_MM
endif
SHMEM_DEF =
ifeq (1,$(BOWTIE_SHARED_MEM))
SHMEM_DEF = -DBOWTIE_SHARED_MEM
endif
PTHREAD_PKG =
PTHREAD_LIB =
ifeq (1,$(MINGW))
PTHREAD_LIB =
else
PTHREAD_LIB = -lpthread
endif
SEARCH_LIBS =
BUILD_LIBS =
INSPECT_LIBS =
ifeq (1,$(MINGW))
BUILD_LIBS =
INSPECT_LIBS =
endif
USE_SRA = 0
SRA_DEF =
SRA_LIB =
SERACH_INC =
ifeq (1,$(USE_SRA))
SRA_DEF = -DUSE_SRA
SRA_LIB = -lncbi-ngs-c++-static -lngs-c++-static -lncbi-vdb-static -ldl
SEARCH_INC += -I$(NCBI_NGS_DIR)/include -I$(NCBI_VDB_DIR)/include
SEARCH_LIBS += -L$(NCBI_NGS_DIR)/lib64 -L$(NCBI_VDB_DIR)/lib64
endif
LIBS = $(PTHREAD_LIB)
SHARED_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
edit.cpp bt2_idx.cpp \
reference.cpp ds.cpp limit.cpp \
random_source.cpp tinythread.cpp
SEARCH_CPPS = qual.cpp pat.cpp \
read_qseq.cpp ref_coord.cpp mask.cpp \
pe.cpp aligner_seed_policy.cpp \
scoring.cpp presets.cpp \
simple_func.cpp random_util.cpp outq.cpp
BUILD_CPPS = diff_sample.cpp
CENTRIFUGE_CPPS_MAIN = $(SEARCH_CPPS) centrifuge_main.cpp
CENTRIFUGE_BUILD_CPPS_MAIN = $(BUILD_CPPS) centrifuge_build_main.cpp
CENTRIFUGE_COMPRESS_CPPS_MAIN = $(BUILD_CPPS) \
aligner_seed.cpp \
aligner_sw.cpp \
aligner_cache.cpp \
dp_framer.cpp \
aligner_bt.cpp sse_util.cpp \
aligner_swsse.cpp \
aligner_swsse_loc_i16.cpp \
aligner_swsse_ee_i16.cpp \
aligner_swsse_loc_u8.cpp \
aligner_swsse_ee_u8.cpp \
scoring.cpp \
mask.cpp \
qual.cpp
CENTRIFUGE_REPORT_CPPS_MAIN=$(BUILD_CPPS)
SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
VERSION = $(shell cat VERSION)
GIT_VERSION = $(VERSION)
#GIT_VERSION = $(shell command -v git 2>&1 > /dev/null && git describe --long --tags --dirty --always --abbrev=10 || cat VERSION)
# Convert BITS=?? to a -m flag
BITS=32
ifeq (x86_64,$(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,$(MINGW))
BITS=64
endif
endif
BITS_FLAG =
ifeq (32,$(BITS))
BITS_FLAG = -m32
endif
ifeq (64,$(BITS))
BITS_FLAG = -m64
endif
SSE_FLAG=-msse2
DEBUG_FLAGS = -O0 -g3 $(BIToS_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) $(EXTRA_FLAGS)\""
NOASSERT_FLAGS = -DNDEBUG
FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
CFLAGS =
#CFLAGS = -fdiagnostics-color=always
ifeq (1,$(USE_SRA))
ifeq (1, $(MACOS))
DEBUG_FLAGS += -mmacosx-version-min=10.6
RELEASE_FLAGS += -mmacosx-version-min=10.6
endif
endif
CENTRIFUGE_BIN_LIST = centrifuge-build-bin \
centrifuge-class \
centrifuge-inspect-bin
CENTRIFUGE_BIN_LIST_AUX = centrifuge-build-bin-debug \
centrifuge-class-debug \
centrifuge-inspect-bin-debug
CENTRIFUGE_SCRIPT_LIST = centrifuge \
centrifuge-build \
centrifuge-inspect \
centrifuge-download \
centrifuge-kreport \
$(wildcard centrifuge-*.pl)
GENERAL_LIST = $(wildcard scripts/*.sh) \
$(wildcard scripts/*.pl) \
$(wildcard *.py) \
$(wildcard *.pl) \
doc/manual.inc.html \
doc/README \
doc/style.css \
$(wildcard example/index/*.cf) \
$(wildcard example/reads/*.fa) \
$(wildcard example/reference/*) \
indices/Makefile \
$(PTHREAD_PKG) \
$(CENTRIFUGE_SCRIPT_LIST) \
AUTHORS \
LICENSE \
NEWS \
MANUAL \
MANUAL.markdown \
TUTORIAL \
VERSION
ifeq (1,$(WINDOWS))
CENTRIFUGE_BIN_LIST := $(CENTRIFUGE_BIN_LIST) centrifuge.bat centrifuge-build.bat centrifuge-inspect.bat
endif
# This is helpful on Windows under MinGW/MSYS, where Make might go for
# the Windows FIND tool instead.
FIND=$(shell which find)
SRC_PKG_LIST = $(wildcard *.h) \
$(wildcard *.hh) \
$(wildcard *.c) \
$(wildcard *.cpp) \
$(wildcard third_party/*.h) \
$(wildcard third_party/*.cpp) \
doc/strip_markdown.pl \
Makefile \
$(GENERAL_LIST)
BIN_PKG_LIST = $(GENERAL_LIST)
.PHONY: all allall both both-debug
all: $(CENTRIFUGE_BIN_LIST)
allall: $(CENTRIFUGE_BIN_LIST) $(CENTRIFUGE_BIN_LIST_AUX)
both: centrifuge-class centrifuge-build-bin
both-debug: centrifuge-class-debug centrifuge-build-bin-debug
DEFS=-fno-strict-aliasing \
-DCENTRIFUGE_VERSION="\"$(GIT_VERSION)\"" \
-DBUILD_HOST="\"`hostname`\"" \
-DBUILD_TIME="\"`date`\"" \
-DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
$(FILE_FLAGS) \
$(CFLAGS) \
$(PREF_DEF) \
$(MM_DEF) \
$(SHMEM_DEF)
#
# centrifuge targets
#
centrifuge-class: centrifuge.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
$(DEFS) $(SRA_DEF) -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \
$(INC) $(SEARCH_INC) \
-o $@ $< \
$(SHARED_CPPS) $(CENTRIFUGE_CPPS_MAIN) \
$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
centrifuge-class-debug: centrifuge.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
$(DEFS) $(SRA_DEF) -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -Wall \
$(INC) $(SRA_LIB) $(SEARCH_INC) \
-o $@ $< \
$(SHARED_CPPS) $(CENTRIFUGE_CPPS_MAIN) \
$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
centrifuge-build-bin: centrifuge_build.cpp $(SHARED_CPPS) $(HEADERS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
$(DEFS) -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(CENTRIFUGE_BUILD_CPPS_MAIN) \
$(LIBS) $(BUILD_LIBS)
centrifuge-build-bin-debug: centrifuge_build.cpp $(SHARED_CPPS) $(HEADERS)
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
$(DEFS) -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -Wall \
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(CENTRIFUGE_BUILD_CPPS_MAIN) \
$(LIBS) $(BUILD_LIBS)
centrifuge-compress-bin: centrifuge_compress.cpp $(SHARED_CPPS) $(CENTRIFUGE_COMPRESS_CPPS_MAIN) $(HEADERS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
$(DEFS) -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(CENTRIFUGE_COMPRESS_CPPS_MAIN) \
$(LIBS) $(BUILD_LIBS)
centrifuge-compress-bin-debug: centrifuge_compress.cpp $(SHARED_CPPS) $(CENTRIFUGE_COMPRESS_CPPS_MAIN) $(HEADERS)
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
$(DEFS) -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -Wall \
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(CENTRIFUGE_COMPRESS_CPPS_MAIN) \
$(LIBS) $(BUILD_LIBS)
centrifuge-report-bin: centrifuge_report.cpp $(SHARED_CPPS) $(CENTRIFUGE_REPORT_CPPS_MAIN) $(HEADERS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
$(DEFS) -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(CENTRIFUGE_REPORT_CPPS_MAIN) \
$(LIBS) $(BUILD_LIBS)
centrifuge-report-bin-debug: centrifuge_report.cpp $(SHARED_CPPS) $(CENTRIFUGE_REPORT_CPPS_MAIN) $(HEADERS)
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
$(DEFS) -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -Wall \
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(CENTRIFUGE_REPORT_CPPS_MAIN) \
$(LIBS) $(BUILD_LIBS)
#centrifuge-RemoveN: centrifuge-RemoveN.cpp
# $(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
# $(DEFS) -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \
# $(INC) \
# -o $@ $<
#
# centrifuge-inspect targets
#
centrifuge-inspect-bin: centrifuge_inspect.cpp $(HEADERS) $(SHARED_CPPS)
$(CXX) $(RELEASE_FLAGS) \
$(RELEASE_DEFS) $(EXTRA_FLAGS) \
$(DEFS) -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -Wall \
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
$(LIBS) $(INSPECT_LIBS)
centrifuge-inspect-bin-debug: centrifuge_inspect.cpp $(HEADERS) $(SHARED_CPPS)
$(CXX) $(DEBUG_FLAGS) \
$(DEBUG_DEFS) $(EXTRA_FLAGS) \
$(DEFS) -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -Wall \
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
$(LIBS) $(INSPECT_LIBS)
centrifuge: ;
centrifuge.bat:
echo "@echo off" > centrifuge.bat
echo "perl %~dp0/centrifuge %*" >> centrifuge.bat
centrifuge-build.bat:
echo "@echo off" > centrifuge-build.bat
echo "python %~dp0/centrifuge-build %*" >> centrifuge-build.bat
centrifuge-inspect.bat:
echo "@echo off" > centrifuge-inspect.bat
echo "python %~dp0/centrifuge-inspect %*" >> centrifuge-inspect.bat
.PHONY: centrifuge-src
centrifuge-src: $(SRC_PKG_LIST)
mkdir .src.tmp
mkdir .src.tmp/centrifuge-$(VERSION)
zip tmp.zip $(SRC_PKG_LIST)
mv tmp.zip .src.tmp/centrifuge-$(VERSION)
cd .src.tmp/centrifuge-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
cd .src.tmp ; zip -r centrifuge-$(VERSION)-source.zip centrifuge-$(VERSION)
cp .src.tmp/centrifuge-$(VERSION)-source.zip .
rm -rf .src.tmp
.PHONY: centrifuge-bin
centrifuge-bin: $(BIN_PKG_LIST) $(CENTRIFUGE_BIN_LIST) $(CENTRIFUGE_BIN_LIST_AUX)
rm -rf .bin.tmp
mkdir .bin.tmp
mkdir .bin.tmp/centrifuge-$(VERSION)
if [ -f centrifuge.exe ] ; then \
zip tmp.zip $(BIN_PKG_LIST) $(addsuffix .exe,$(CENTRIFUGE_BIN_LIST) $(CENTRIFUGE_BIN_LIST_AUX)) ; \
else \
zip tmp.zip $(BIN_PKG_LIST) $(CENTRIFUGE_BIN_LIST) $(CENTRIFUGE_BIN_LIST_AUX) ; \
fi
mv tmp.zip .bin.tmp/centrifuge-$(VERSION)
cd .bin.tmp/centrifuge-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
cd .bin.tmp ; zip -r centrifuge-$(VERSION)-$(BITS).zip centrifuge-$(VERSION)
cp .bin.tmp/centrifuge-$(VERSION)-$(BITS).zip .
rm -rf .bin.tmp
.PHONY: doc
doc: doc/manual.inc.html MANUAL
doc/manual.inc.html: MANUAL.markdown
pandoc -T "Centrifuge Manual" -o $@ \
--from markdown --to HTML --toc $^
perl -i -ne \
'$$w=0 if m|^</body>|;print if $$w;$$w=1 if m|^<body>|;' $@
MANUAL: MANUAL.markdown
perl doc/strip_markdown.pl < $^ > $@
prefix=/usr/local
.PHONY: install
install: all
mkdir -p $(prefix)/bin
mkdir -p $(prefix)/share/centrifuge/indices
install -m 0644 indices/Makefile $(prefix)/share/centrifuge/indices
install -d -m 0755 $(prefix)/share/centrifuge/doc
install -m 0644 doc/* $(prefix)/share/centrifuge/doc
for file in $(CENTRIFUGE_BIN_LIST) $(CENTRIFUGE_SCRIPT_LIST); do \
install -m 0755 $$file $(prefix)/bin ; \
done
.PHONY: uninstall
uninstall: all
for file in $(CENTRIFUGE_BIN_LIST) $(CENTRIFUGE_SCRIPT_LIST); do \
rm -v $(prefix)/bin/$$file ; \
rm -v $(prefix)/share/centrifuge; \
done
.PHONY: clean
clean:
rm -f $(CENTRIFUGE_BIN_LIST) $(CENTRIFUGE_BIN_LIST_AUX) \
$(addsuffix .exe,$(CENTRIFUGE_BIN_LIST) $(CENTRIFUGE_BIN_LIST_AUX)) \
centrifuge-src.zip centrifuge-bin.zip
rm -f core.* .tmp.head
rm -rf *.dSYM
push-doc: doc/manual.inc.html
scp doc/*.*html igm1:/data1/igm3/www/ccb.jhu.edu/html/software/centrifuge/