Makefile

   1 #
   2 # Makefile for bowtie, bowtie-build, bowtie-inspect
   3 #
   4
   5 SEQAN_DIR = SeqAn-1.1
   6 SEQAN_INC = -I $(SEQAN_DIR)
   7 INC = $(SEQAN_INC)
   8 GCC_PREFIX = $(shell dirname `which gcc`)
   9 GCC_SUFFIX =
  10 CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
  11 CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
  12 CXX = $(CPP)
  13 HEADERS = $(wildcard *.h)
  14 BOWTIE_PTHREADS = 1
  15 BOWTIE_MM = 1
  16 BOWTIE_SHARED_MEM = 1
  17 EXTRA_FLAGS =
  18 EXTRA_CFLAGS =
  19 EXTRA_CXXFLAGS =
  20 CFLAGS += $(EXTRA_CFLAGS)
  21 CXXFLAGS += $(EXTRA_CXXFLAGS)
  22
  23 # Detect Cygwin or MinGW
  24 WINDOWS = 0
  25 ifneq (,$(findstring CYGWIN,$(shell uname)))
  26 WINDOWS = 1
  27 # POSIX memory-mapped files not currently supported on Windows
  28 BOWTIE_MM = 0
  29 BOWTIE_SHARED_MEM = 0
  30 else
  31 ifneq (,$(findstring MINGW,$(shell uname)))
  32 WINDOWS = 1
  33 # POSIX memory-mapped files not currently supported on Windows
  34 BOWTIE_MM = 0
  35 BOWTIE_SHARED_MEM = 0
  36 endif
  37 endif
  38
  39 MACOS = 0
  40 ifneq (,$(findstring Darwin,$(shell uname)))
  41 MACOS = 1
  42 endif
  43
  44 LINUX = 0
  45 ifneq (,$(findstring Linux,$(shell uname)))
  46 LINUX = 1
  47 EXTRA_FLAGS += -Wl,--hash-style=both
  48 endif
  49
  50 MM_DEF =
  51 ifeq (1,$(BOWTIE_MM))
  52 MM_DEF = -DBOWTIE_MM
  53 endif
  54 SHMEM_DEF =
  55 ifeq (1,$(BOWTIE_SHARED_MEM))
  56 SHMEM_DEF = -DBOWTIE_SHARED_MEM
  57 endif
  58 PTHREAD_PKG =
  59 PTHREAD_LIB =
  60 PTHREAD_DEF =
  61 ifeq (1,$(BOWTIE_PTHREADS))
  62 PTHREAD_DEF = -DBOWTIE_PTHREADS
  63 ifeq (1,$(WINDOWS))
  64 # pthreads for windows forces us to be specific about the library
  65 PTHREAD_LIB = -L . -lpthreadGC2
  66 PTHREAD_PKG = pthreadGC2.dll
  67 else
  68 # There's also -pthread, but that only seems to work on Linux
  69 PTHREAD_LIB = -lpthread
  70 endif
  71 endif
  72
  73 PREFETCH_LOCALITY = 2
  74 PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
  75
  76 LIBS =
  77 SEARCH_LIBS = $(PTHREAD_LIB)
  78 BUILD_LIBS =
  79
  80 OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp \
  81              edit.cpp ebwt.cpp
  82 SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp \
  83               log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp \
  84               color.cpp color_dec.cpp hit.cpp
  85 SEARCH_CPPS_MAIN = $(SEARCH_CPPS) bowtie_main.cpp
  86
  87 BUILD_CPPS =
  88 BUILD_CPPS_MAIN = $(BUILD_CPPS) bowtie_build_main.cpp
  89
  90 SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
  91 VERSION = $(shell cat VERSION)
  92
  93 # Convert BITS=?? to a -m flag
  94 BITS_FLAG =
  95 ifeq (32,$(BITS))
  96 BITS_FLAG = -m32
  97 endif
  98 ifeq (64,$(BITS))
  99 BITS_FLAG = -m64
 100 endif
 101
 102 # Convert CHUD=1 to CHUD-related flags
 103 CHUD=0
 104 CHUD_DEF =
 105 ifeq (1,$(CHUD))
 106 EXTRA_FLAGS += -g3
 107 ifeq (1,$(MACOS))
 108 CHUD_DEF = -F/System/Library/PrivateFrameworks -weak_framework CHUD -DCHUD_PROFILING
 109 endif
 110 endif
 111
 112 DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG)
 113 RELEASE_FLAGS = -O3 $(BITS_FLAG)
 114 NOASSERT_FLAGS = -DNDEBUG
 115 FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
 116
 117 BIN_LIST = bowtie-build \
 118            bowtie \
 119            bowtie-inspect
 120 BIN_LIST_AUX = bowtie-build-debug \
 121                bowtie-debug \
 122                bowtie-inspect-debug
 123
 124 GENERAL_LIST = $(wildcard scripts/*.sh) \
 125                $(wildcard scripts/*.pl) \
 126                $(wildcard indexes/e_coli*) \
 127                $(wildcard genomes/NC_008253.fna) \
 128                $(wildcard reads/e_coli_1000.*) \
 129                $(wildcard reads/e_coli_1000_*) \
 130                doc/manual.html \
 131                doc/README \
 132                doc/style.css \
 133                reads/e_coli_10000snp.fa \
 134                reads/e_coli_10000snp.fq \
 135                $(PTHREAD_PKG) \
 136                AUTHORS \
 137                COPYING \
 138                NEWS \
 139                MANUAL \
 140                MANUAL.markdown \
 141                TUTORIAL \
 142                VERSION
 143
 144 # This is helpful on Windows under MinGW/MSYS, where Make might go for
 145 # the Windows FIND tool instead.
 146 FIND=$(shell which find)
 147
 148 SRC_PKG_LIST = $(wildcard *.h) \
 149                $(wildcard *.hh) \
 150                $(wildcard *.c) \
 151                $(wildcard *.cpp) \
 152                $(shell $(FIND) SeqAn-1.1 -name "*.h") \
 153                $(shell $(FIND) SeqAn-1.1 -name "*.txt") \
 154                doc/strip_markdown.pl \
 155                Makefile \
 156                $(GENERAL_LIST)
 157
 158 BIN_PKG_LIST = $(GENERAL_LIST)
 159
 160 all: $(BIN_LIST)
 161
 162 allall: $(BIN_LIST) $(BIN_LIST_AUX)
 163
 164 DEFS=-fno-strict-aliasing \
 165      -DBOWTIE_VERSION="\"`cat VERSION`\"" \
 166      -DBUILD_HOST="\"`hostname`\"" \
 167      -DBUILD_TIME="\"`date`\"" \
 168      -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
 169      $(FILE_FLAGS) \
 170      $(PTHREAD_DEF) \
 171      $(PREF_DEF) \
 172      $(MM_DEF) \
 173      $(SHMEM_DEF) \
 174      $(CHUD_DEF)
 175
 176 define checksum
 177   cat $^ | md5sum | awk '{print $$1}' > .$@.md5
 178 endef
 179
 180 ALL_FLAGS=$(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)
 181 DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\""
 182 RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\""
 183
 184 #
 185 # bowtie-build targets
 186 #
 187
 188 bowtie-build: ebwt_build.cpp $(OTHER_CPPS) $(HEADERS)
 189         $(checksum)
 190         $(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(ALL_FLAGS) \
 191                 -DEBWT_BUILD_HASH=`cat .$@.md5` \
 192                 $(DEFS) $(NOASSERT_FLAGS) -Wall \
 193                 $(INC) \
 194                 -o $@ $< \
 195                 $(OTHER_CPPS) $(BUILD_CPPS_MAIN) \
 196                 $(LIBS) $(BUILD_LIBS)
 197
 198 bowtie-build_prof: ebwt_build.cpp $(OTHER_CPPS) $(HEADERS)
 199         $(checksum)
 200         $(CXX) $(RELEASE_FLAGS) -pg -p -g3 $(RELEASE_DEFS) $(ALL_FLAGS) \
 201                 -DEBWT_BUILD_HASH=`cat .$@.md5` \
 202                 $(DEFS) $(NOASSERT_FLAGS) -Wall \
 203                 $(INC) \
 204                 -o $@ $< \
 205                 $(OTHER_CPPS) $(BUILD_CPPS_MAIN) \
 206                 $(LIBS) $(BUILD_LIBS)
 207
 208 bowtie-build-debug: ebwt_build.cpp $(OTHER_CPPS) $(HEADERS)
 209         $(checksum)
 210         $(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(ALL_FLAGS) \
 211                 -DEBWT_BUILD_HASH=`cat .$@.md5` \
 212                 $(DEFS) -Wall \
 213                 $(INC) \
 214                 -o $@ $< \
 215                 $(OTHER_CPPS) $(BUILD_CPPS_MAIN) \
 216                 $(LIBS) $(BUILD_LIBS)
 217
 218 #
 219 # bowtie targets
 220 #
 221
 222 bowtie: ebwt_search.cpp $(SEARCH_CPPS) $(OTHER_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
 223         $(checksum)
 224         $(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(ALL_FLAGS) \
 225                 -DEBWT_SEARCH_HASH=`cat .$@.md5` \
 226                 $(DEFS) $(NOASSERT_FLAGS) -Wall \
 227                 $(INC) \
 228                 -o $@ $< \
 229                 $(OTHER_CPPS) $(SEARCH_CPPS_MAIN) \
 230                 $(LIBS) $(SEARCH_LIBS)
 231
 232 bowtie_prof: ebwt_search.cpp $(SEARCH_CPPS) $(OTHER_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
 233         $(checksum)
 234         $(CXX) $(RELEASE_FLAGS) \
 235                 $(RELEASE_DEFS) -pg -p -g3 $(ALL_FLAGS) \
 236                 -DEBWT_SEARCH_HASH=`cat .$@.md5` \
 237                 $(DEFS) $(NOASSERT_FLAGS) -Wall \
 238                 $(INC) \
 239                 -o $@ $< \
 240                 $(OTHER_CPPS) $(SEARCH_CPPS_MAIN) \
 241                 $(LIBS) $(SEARCH_LIBS)
 242
 243 bowtie-debug: ebwt_search.cpp $(SEARCH_CPPS) $(OTHER_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
 244         $(checksum)
 245         $(CXX) $(DEBUG_FLAGS) \
 246                 $(DEBUG_DEFS) $(ALL_FLAGS) \
 247                 -DEBWT_SEARCH_HASH=`cat .$@.md5` \
 248                 $(DEFS) -Wall \
 249                 $(INC) \
 250                 -o $@ $< \
 251                 $(OTHER_CPPS) $(SEARCH_CPPS_MAIN) \
 252                 $(LIBS) $(SEARCH_LIBS)
 253
 254 #
 255 # bowtie-inspect targets
 256 #
 257
 258 bowtie-inspect: bowtie_inspect.cpp $(HEADERS) $(OTHER_CPPS)
 259         $(checksum)
 260         $(CXX) $(RELEASE_FLAGS) \
 261                 $(RELEASE_DEFS) $(ALL_FLAGS) \
 262                 -DEBWT_INSPECT_HASH=`cat .$@.md5` \
 263                 $(DEFS) -Wall \
 264                 $(INC) -I . \
 265                 -o $@ $< \
 266                 $(OTHER_CPPS) \
 267                 $(LIBS)
 268
 269 bowtie-inspect-debug: bowtie_inspect.cpp $(HEADERS) $(OTHER_CPPS)
 270         $(checksum)
 271         $(CXX) $(DEBUG_FLAGS) \
 272                 $(DEBUG_DEFS) $(ALL_FLAGS) \
 273                 -DEBWT_INSPECT_HASH=`cat .$@.md5` \
 274                 $(DEFS) -Wall \
 275                 $(INC) -I . \
 276                 -o $@ $< \
 277                 $(OTHER_CPPS) \
 278                 $(LIBS)
 279
 280 chaincat: chaincat.cpp hit_set.h filebuf.h hit_set.cpp alphabet.h alphabet.c
 281         $(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(ALL_FLAGS) -Wall $(INC) -I . -o $@ $< hit_set.cpp alphabet.c
 282
 283 bowtie-src.zip: $(SRC_PKG_LIST)
 284         chmod a+x scripts/*.sh scripts/*.pl
 285         mkdir .src.tmp
 286         mkdir .src.tmp/bowtie-$(VERSION)
 287         zip tmp.zip $(SRC_PKG_LIST)
 288         mv tmp.zip .src.tmp/bowtie-$(VERSION)
 289         cd .src.tmp/bowtie-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
 290         cd .src.tmp ; zip -r $@ bowtie-$(VERSION)
 291         cp .src.tmp/$@ .
 292         rm -rf .src.tmp
 293
 294 bowtie-bin.zip: $(BIN_PKG_LIST) $(BIN_LIST) $(BIN_LIST_AUX)
 295         chmod a+x scripts/*.sh scripts/*.pl
 296         rm -rf .bin.tmp
 297         mkdir .bin.tmp
 298         mkdir .bin.tmp/bowtie-$(VERSION)
 299         if [ -f bowtie.exe ] ; then \
 300                 zip tmp.zip $(BIN_PKG_LIST) $(addsuffix .exe,$(BIN_LIST) $(BIN_LIST_AUX)) ; \
 301         else \
 302                 zip tmp.zip $(BIN_PKG_LIST) $(BIN_LIST) $(BIN_LIST_AUX) ; \
 303         fi
 304         mv tmp.zip .bin.tmp/bowtie-$(VERSION)
 305         cd .bin.tmp/bowtie-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
 306         cd .bin.tmp ; zip -r $@ bowtie-$(VERSION)
 307         cp .bin.tmp/$@ .
 308         rm -rf .bin.tmp
 309
 310 .PHONY: doc
 311 doc: doc/manual.html MANUAL
 312
 313 doc/manual.html: MANUAL.markdown
 314         echo "<h1>Table of Contents</h1>" > .tmp.head
 315         pandoc -T "Bowtie Manual" -B .tmp.head \
 316                --css style.css -o $@ \
 317                --from markdown --to HTML \
 318                --table-of-contents $^
 319
 320 MANUAL: MANUAL.markdown
 321         perl doc/strip_markdown.pl < $^ > $@
 322
 323 .PHONY: clean
 324 clean:
 325         rm -f $(BIN_LIST) $(BIN_LIST_AUX) \
 326         bowtie_prof \
 327         $(addsuffix .exe,$(BIN_LIST) $(BIN_LIST_AUX) bowtie_prof) \
 328         bowtie-src.zip bowtie-bin.zip
 329         rm -f core.*