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Makefile
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Makefile
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#
# Copyright 2018, Daehwan Kim <[email protected]>
#
# This file is part of CMA.
#
# CMA 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.
#
# CMA 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 HISAT. If not, see <http://www.gnu.org/licenses/>.
#
#
# Makefile for hisat2-align, hisat2-build, hisat2-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 = $(wildcard *.h)
BOWTIE_MM = 1
BOWTIE_SHARED_MEM = 0
# Detect Cygwin or MinGW
WINDOWS = 0
CYGWIN = 0
MINGW = 0
ifneq (,$(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,$(shell uname)))
MACOS = 1
endif
EXTRA_FLAGS += -DPOPCNT_CAPABILITY
INC += -I third_party
MM_DEF =
ifeq (1,$(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
SERACH_INC =
LIBS = $(PTHREAD_LIB) -ltiff
SHARED_CPPS =
SEARCH_CPPS =
CMA_CPPS_MAIN = $(SEARCH_CPPS) hisat2_main.cpp
CMA_BUILD_CPPS_MAIN = $(BUILD_CPPS) hisat2_build_main.cpp
SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
VERSION = $(shell cat VERSION)
ifeq (1,$(MACOS))
LIBS += -framework Accelerate
LIBS += -framework OpenCL
EXTRA_FLAGS += -I/Systm/Library/Frameworks/Accelerate.framework/Versions/Current/Headers
else
DYNAMIC_LIBS += -lOpenCL
endif
# 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) $(EXTRA_FLAGS)\""
NOASSERT_FLAGS = -DNDEBUG
FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
ifeq (1,$(USE_SRA))
ifeq (1, $(MACOS))
DEBUG_FLAGS += -mmacosx-version-min=10.6
RELEASE_FLAGS += -mmacosx-version-min=10.6
endif
endif
CMA_BIN_LIST = cma-bin
CMA_BIN_LIST_AUX = cma-bin-debug
GENERAL_LIST = $(wildcard scripts/*.sh) \
$(wildcard scripts/*.pl) \
$(wildcard *.py) \
$(wildcard hisatgenotype_modules/*.py) \
$(wildcard hisatgenotype_scripts/*.py) \
doc/manual.inc.html \
doc/README \
doc/style.css \
$(wildcard example/index/*.ht2) \
$(wildcard example/reads/*.fa) \
example/reference/22_20-21M.fa \
example/reference/22_20-21M.snp \
$(PTHREAD_PKG) \
cma \
cma-bin \
AUTHORS \
LICENSE \
NEWS \
MANUAL \
MANUAL.markdown \
TUTORIAL \
VERSION
ifeq (1,$(WINDOWS))
CMA_BIN_LIST := $(CMA_BIN_LIST) hisat2.bat hisat2-build.bat hisat2-inspect.bat
endif
# This is helpful on Windows under MinGW/MSYS, where Make might go for
# the Windows FIND tool instead.
FIND=$(shell which find)
SRC_PKG_LIST = $(wildcard *.h) \
$(wildcard *.hh) \
$(wildcard *.c) \
$(wildcard *.cpp) \
doc/strip_markdown.pl \
Makefile \
$(GENERAL_LIST)
BIN_PKG_LIST = $(GENERAL_LIST)
.PHONY: all allall both both-debug
all: $(CMA_BIN_LIST)
allall: $(CMA_BIN_LIST) $(CMA_BIN_LIST_AUX)
both: cma-bin
both-debug: cma-bin-debug
DEFS=-fno-strict-aliasing \
-DCMA_VERSION="\"`cat VERSION`\"" \
-DBUILD_HOST="\"`hostname`\"" \
-DBUILD_TIME="\"`date`\"" \
-DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
$(FILE_FLAGS) \
$(PREF_DEF) \
$(MM_DEF) \
$(SHMEM_DEF)
cma-bin: cma.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
$(DEFS) $(NOASSERT_FLAGS) -Wall \
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
$(LIBS) $(SEARCH_LIBS)
cma-bin-debug: cma.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(DEBUG_FLAGS) \
$(DEBUG_DEFS) $(EXTRA_FLAGS) \
$(DEFS) -Wall \
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
$(LIBS) $(SEARCH_LIBS)
cma: ;
cma.bat:
echo "@echo off" > hisat2.bat
echo "perl %~dp0/cma %*" >> hisat2.bat
hisat2-build.bat:
echo "@echo off" > hisat2-build.bat
echo "python %~dp0/hisat2-build %*" >> hisat2-build.bat
hisat2-inspect.bat:
echo "@echo off" > hisat2-inspect.bat
echo "python %~dp0/hisat2-inspect %*" >> hisat2-inspect.bat
.PHONY: cma-src
cma-src-pkg: $(SRC_PKG_LIST)
chmod a+x scripts/*.sh scripts/*.pl
mkdir .src.tmp
mkdir .src.tmp/hisat2-$(VERSION)
zip tmp.zip $(SRC_PKG_LIST)
mv tmp.zip .src.tmp/hisat2-$(VERSION)
cd .src.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
cd .src.tmp ; zip -r hisat2-$(VERSION)-source.zip hisat2-$(VERSION)
cp .src.tmp/hisat2-$(VERSION)-source.zip .
rm -rf .src.tmp
.PHONY: cma-bin
cma-bin-pkg: $(BIN_PKG_LIST) $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)
chmod a+x scripts/*.sh scripts/*.pl
rm -rf .bin.tmp
mkdir .bin.tmp
mkdir .bin.tmp/hisat2-$(VERSION)
if [ -f hisat2.exe ] ; then \
zip tmp.zip $(BIN_PKG_LIST) $(addsuffix .exe,$(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)) ; \
else \
zip tmp.zip $(BIN_PKG_LIST) $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) ; \
fi
mv tmp.zip .bin.tmp/hisat2-$(VERSION)
cd .bin.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
cd .bin.tmp ; zip -r hisat2-$(VERSION)-$(BITS).zip hisat2-$(VERSION)
cp .bin.tmp/hisat2-$(VERSION)-$(BITS).zip .
rm -rf .bin.tmp
.PHONY: doc
doc: doc/manual.inc.html MANUAL
doc/manual.inc.html: MANUAL.markdown
pandoc -T "HISAT2 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 < $^ > $@
.PHONY: clean
clean:
rm -f $(CMA_BIN_LIST) $(CMA_BIN_LIST_AUX) \
$(addsuffix .exe,$(CMA_BIN_LIST) $(CMA_BIN_LIST_AUX)) \
cma-src.zip cma-bin.zip
rm -f core.* .tmp.head
rm -rf *.dSYM
.PHONY: push-doc
push-doc: doc/manual.inc.html
scp doc/*.*html doc/indexes.txt salz-dmz:/ccb/salz7-data/www/ccb.jhu.edu/html/software/hisat2/