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Makefile
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#
# Copyright (c) 2006-2014 Gordon Gremme <[email protected]>
# Copyright (c) 2008-2014 Sascha Steinbiss <[email protected]>
# Copyright (c) 2006-2013 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#
INCLUDEOPT:=-I$(CURDIR)/src -I$(CURDIR)/obj
ifeq ($(shell pkg-config --version > /dev/null 2> /dev/null; echo $$?),0)
HAS_PKGCONFIG:=yes
# Fix for Mac OS X manual building with Homebrew
OLD_PKG_CONFIG_PATH:=$(PKG_CONFIG_PATH)
OVERRIDE_PC_PATH:=PKG_CONFIG_PATH=$(OLD_PKG_CONFIG_PATH):/usr/local/lib/pkgconfig:/opt/X11/lib/pkgconfig
else
HAS_PKGCONFIG:=no
endif
# add necessary shared lib dependencies instead of building them ourselves
ifeq ($(useshared),yes)
ifeq ($(HAS_PKGCONFIG),yes)
DEPLIBS:=-lbz2 \
$(shell $(OVERRIDE_PC_PATH) pkg-config --libs zlib) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --libs expat) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --libs lua-5.1) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --libs lua5.1-lpeg) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --libs lua5.1-md5) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --libs lua5.1-filesystem) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --libs lua5.1-des56) \
-lbam \
$(shell $(OVERRIDE_PC_PATH) pkg-config --libs tre) \
-lm -lpthread
INCLUDEOPT+=$(shell $(OVERRIDE_PC_PATH) pkg-config --cflags zlib) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --cflags expat) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --cflags lua-5.1) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --cflags lua5.1-lpeg) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --cflags lua5.1-md5) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --cflags lua5.1-filesystem) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --cflags lua5.1-des56) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --cflags tre)
else
# Requested the use of shared libraries without having pkg-config.
# You are on your own. Good luck.
DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
-llua5.1-filesystem -llua5.1-des56 -lbam -ltre -lm -lpthread
endif
else
DEPLIBS:=
INCLUDEOPT+=-I$(CURDIR)/src/external/zlib-1.2.8 \
-I$(CURDIR)/src/external/md5-1.2/src \
-I$(CURDIR)/src/external/lua-5.1.5/src \
-I$(CURDIR)/src/external/luafilesystem-1.5.0/src \
-I$(CURDIR)/src/external/lpeg-0.10.2 \
-I$(CURDIR)/src/external/expat-2.0.1/lib \
-I$(CURDIR)/src/external/bzip2-1.0.6 \
-I$(CURDIR)/src/external/samtools-0.1.18 \
-I$(CURDIR)/src/external/sqlite-3.33.0 \
-I$(CURDIR)/src/external/tre/include
endif
ifneq ($(cairo),no)
# XXX: check for existence of packages, and emit warning and disable cairo
# if packages are not available
ifeq ($(HAS_PKGCONFIG),yes)
INCLUDEOPT+=$(shell $(OVERRIDE_PC_PATH) pkg-config --silence-errors --cflags-only-I pango) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --silence-errors --cflags-only-I cairo) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --silence-errors --cflags-only-I pangocairo) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --silence-errors --cflags-only-I glib-2.0)
endif
GOTAGS:=-tags cairo
endif
ifneq ($(fpic),no)
FPIC:=-fPIC
endif
# these variables are exported by the configuration script
ifndef CC
CC:=gcc
endif
ifndef CXX
CXX:=g++
endif
EXP_CFLAGS:=$(CFLAGS)
EXP_LDFLAGS:=$(LDFLAGS)
EXP_CXXFLAGS:=$(CXXFLAGS)
EXP_CPPFLAGS:=$(CPPFLAGS)
EXP_LDLIBS:=$(LIBS) -lm
# ...while those starting with GT_ are for internal purposes only
GT_CFLAGS:=-g -Wall -Wunused-parameter -pipe $(FPIC) -Wpointer-arith -Wno-unknown-pragmas
# expat needs -DHAVE_MEMMOVE
# zlib needs -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN
EXT_FLAGS:= -DHAVE_MEMMOVE -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN
EXP_CPPFLAGS+=-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 $(EXT_FLAGS)
GT_CPPFLAGS:=$(INCLUDEOPT)
GT_CXXFLAGS:=-g -pipe
GT_LDFLAGS:=-Llib
STEST_FLAGS:=
EXP_LDFLAGS+=$(foreach dir, \
$(shell test -d /usr/local/lib && echo /usr/local/lib ; \
test -d /usr/X11R6/lib && echo /usr/X11R6/lib ; \
test -d /opt/local/lib && echo /opt/local/lib),-L$(dir))
BUILDSTAMP:=$(shell date +'"%Y-%m-%d %H:%M:%S"')
# try to set RANLIB automatically
SYSTEM?=$(shell uname -s)
MACHINE:=$(shell uname -m)
ifeq ($(SYSTEM),Darwin)
RANLIB:=ranlib
NO_STATIC_LINKING:=defined
SHARED:=-dynamiclib -undefined dynamic_lookup
SHARED_OBJ_NAME_EXT:=.dylib
ifeq ($(universal),yes)
MACHINE:="Universal_Binary"
GT_CFLAGS+=-arch i386 -arch ppc -arch_errors_fatal
GT_LDFLAGS+=-arch i386 -arch ppc -arch_errors_fatal
endif
ifeq ($(ppc),yes)
MACHINE:="Power_Macintosh"
GT_CFLAGS+=-arch ppc -arch_errors_fatal
GT_LDFLAGS+=-arch ppc -arch_errors_fatal
endif
# these tests are disabled for now on Mac
TEST_KEYWORDS:=-keywords \
'not gt_ruby and not gt_sketch and not gt_seqlensort'
else
SHARED_OBJ_NAME_EXT:=.so
SHARED:=-shared
endif
# compiled executables
GTMAIN_SRC:=src/gt.c src/gtr.c src/gtt.c src/interactive.c
GTMAIN_OBJ:=$(GTMAIN_SRC:%.c=obj/%.o)
GTMAIN_DEP:=$(GTMAIN_SRC:%.c=obj/%.d)
EXAMPLES_SRC:=src/example.c
EXAMPLES_DEP:=$(EXAMPLES_SRC:%.c=obj/%.d)
TOOLS_SRC:=$(sort $(wildcard src/tools/*.c))
TOOLS_OBJ:=$(TOOLS_SRC:%.c=obj/%.o)
TOOLS_DEP:=$(TOOLS_SRC:%.c=obj/%.d)
EXPAT_DIR:=src/external/expat-2.0.1/lib
LIBEXPAT_SRC:=$(EXPAT_DIR)/xmlparse.c $(EXPAT_DIR)/xmlrole.c \
$(EXPAT_DIR)/xmltok.c
LIBEXPAT_OBJ:=$(LIBEXPAT_SRC:%.c=obj/%.o)
LIBEXPAT_DEP:=$(LIBEXPAT_SRC:%.c=obj/%.d)
TRE_DIR:=src/external/tre/lib
TRE_CPPFLAGS=-I$(CURDIR)/src/external/tre/include/tre
LIBTRE_SRC:=$(TRE_DIR)/regcomp.c $(TRE_DIR)/regerror.c $(TRE_DIR)/regexec.c \
$(TRE_DIR)/tre-ast.c $(TRE_DIR)/tre-compile.c \
$(TRE_DIR)/tre-filter.c $(TRE_DIR)/tre-match-backtrack.c \
$(TRE_DIR)/tre-match-parallel.c $(TRE_DIR)/tre-mem.c \
$(TRE_DIR)/tre-parse.c $(TRE_DIR)/tre-stack.c $(TRE_DIR)/xmalloc.c
LIBTRE_OBJ:=$(LIBTRE_SRC:%.c=obj/%.o)
LIBTRE_DEP:=$(LIBTRE_SRC:%.c=obj/%.d)
LIBLUA_SRC=src/lualib.c\
src/external/md5-1.2/src/md5.c\
src/external/md5-1.2/src/md5lib.c\
src/external/md5-1.2/src/des56.c\
src/external/md5-1.2/src/ldes56.c\
src/external/md5-1.2/src/compat-5.2.c\
src/external/luafilesystem-1.5.0/src/lfs.c\
src/external/lpeg-0.10.2/lpeg.c
LIBLUA_OBJ:=$(LIBLUA_SRC:%.c=obj/%.o)
LIBLUA_DEP:=$(LIBLUA_SRC:%.c=obj/%.d)
LUAMAIN_SRC:=src/external/lua-5.1.5/etc/all.c
LUAMAIN_OBJ:=$(LUAMAIN_SRC:%.c=obj/%.o)
LUAMAIN_DEP:=$(LUAMAIN_SRC:%.c=obj/%.d)
BZ2_DIR:=src/external/bzip2-1.0.6
LIBBZ2_SRC:=$(BZ2_DIR)/blocksort.c $(BZ2_DIR)/huffman.c $(BZ2_DIR)/crctable.c \
$(BZ2_DIR)/randtable.c $(BZ2_DIR)/compress.c \
$(BZ2_DIR)/decompress.c $(BZ2_DIR)/bzlib.c
LIBBZ2_OBJ:=$(LIBBZ2_SRC:%.c=obj/%.o)
LIBBZ2_DEP:=$(LIBBZ2_SRC:%.c=obj/%.d)
SQLITE3_DIR:=src/external/sqlite-3.33.0
SQLITE3_SRC:=$(SQLITE3_DIR)/sqlite3.c
SQLITE3_OBJ:=$(SQLITE3_SRC:%.c=obj/%.o)
SQLITE3_DEP:=$(SQLITE3_SRC:%.c=obj/%.d)
ZLIB_DIR:=src/external/zlib-1.2.8
ZLIB_SRC:=$(ZLIB_DIR)/adler32.c $(ZLIB_DIR)/compress.c $(ZLIB_DIR)/crc32.c \
$(ZLIB_DIR)/gzclose.c $(ZLIB_DIR)/gzlib.c $(ZLIB_DIR)/gzread.c \
$(ZLIB_DIR)/gzwrite.c $(ZLIB_DIR)/uncompr.c $(ZLIB_DIR)/deflate.c \
$(ZLIB_DIR)/trees.c $(ZLIB_DIR)/zutil.c $(ZLIB_DIR)/inflate.c \
$(ZLIB_DIR)/infback.c $(ZLIB_DIR)/inftrees.c $(ZLIB_DIR)/inffast.c
ZLIB_OBJ:=$(ZLIB_SRC:%.c=obj/%.o)
ZLIB_DEP:=$(ZLIB_SRC:%.c=obj/%.d)
SAMTOOLS_DIR:=src/external/samtools-0.1.18
SAMTOOLS_SRC:=$(SAMTOOLS_DIR)/bgzf.c \
$(SAMTOOLS_DIR)/kstring.c \
$(SAMTOOLS_DIR)/bam_aux.c \
$(SAMTOOLS_DIR)/bam.c \
$(SAMTOOLS_DIR)/bam_import.c \
$(SAMTOOLS_DIR)/sam.c \
$(SAMTOOLS_DIR)/bam_index.c \
$(SAMTOOLS_DIR)/bam_pileup.c \
$(SAMTOOLS_DIR)/bam_lpileup.c \
$(SAMTOOLS_DIR)/bam_md.c \
$(SAMTOOLS_DIR)/razf.c \
$(SAMTOOLS_DIR)/faidx.c \
$(SAMTOOLS_DIR)/bedidx.c \
$(SAMTOOLS_DIR)/knetfile.c \
$(SAMTOOLS_DIR)/bam_sort.c \
$(SAMTOOLS_DIR)/sam_header.c \
$(SAMTOOLS_DIR)/bam_reheader.c \
$(SAMTOOLS_DIR)/kprobaln.c \
$(SAMTOOLS_DIR)/bam_cat.c
SAMTOOLS_OBJ:=$(SAMTOOLS_SRC:%.c=obj/%.o)
SAMTOOLS_DEP:=$(SAMTOOLS_SRC:%.c=obj/%.d)
EXP_LDLIBS += $(DEPLIBS)
GTSHAREDLIB_LIBDEP += $(DEPLIBS)
WWWBASEDIR=/var/www/servers
# process arguments
ifeq ($(assert),no)
EXP_CPPFLAGS += -DNDEBUG
endif
ifeq ($(shell hmmscan -h > /dev/null 2> /dev/null; echo $$?),0)
STEST_FLAGS += -hmmer
endif
ifeq ($(cov),yes)
export CCACHE_DISABLE # ccache cannot handle coverage objects
GT_CFLAGS += -fprofile-arcs -ftest-coverage
GT_LDFLAGS += -fprofile-arcs -ftest-coverage
STEST_FLAGS += -gcov
opt=no
# hacks to link shared libs with cov=yes
ifeq ($(SYSTEM),Linux)
GT_LDFLAGS += -fprofile-arcs -ftest-coverage
endif
ifeq ($(MACHINE),amd64)
GT_LDFLAGS += $(FPIC)
endif
endif
ifneq ($(opt),no)
ifeq ($(findstring clang,$(CC)),clang)
ifeq ($(lto),yes)
# clang/LLVM supports link-time optimization with -O4
# Note that on Linux this usually requires additional configuration of
# LLVM! Consult http://llvm.org/docs/GoldPlugin.html if problems arise.
GT_CFLAGS += -O4
GT_CXXFLAGS += -O4
else
GT_CFLAGS += -O3
GT_CXXFLAGS += -O3
endif
else
GT_CFLAGS += -O3
GT_CXXFLAGS += -O3
endif
endif
ifeq ($(prof),yes)
GT_CFLAGS += -pg
GT_LDFLAGS += -pg
endif
ifeq ($(curl),yes)
EXP_CPPFLAGS += -DCURLDEF
GT_CPPFLAGS += -I/usr/include/curl -I/usr/local/include/curl
EXP_LDLIBS += -lcurl
endif
ifdef testthreads
STEST_FLAGS += -threads $(testthreads)
endif
ifdef gttestdata
STEST_FLAGS += -gttestdata $(gttestdata)
endif
ifeq ($(memcheck),yes)
STEST_FLAGS += -memcheck
endif
ifeq ($(64bit),yes)
ifeq ($(32bit),yes)
$(error Variables set contradictory: 64bit/32bit)
endif
endif
ifeq ($(64bit),no)
ifeq ($(32bit),no)
$(error Variables set contradictory: 64bit/32bit)
endif
endif
# system specific stuff (concerning 64bit compilation)
ifeq ($(SYSTEM),Darwin)
ifeq ($(64bit),no)
m32=yes
else
ifeq ($(32bit),yes)
m32=yes
else
m64=yes
endif
endif
endif
ifneq ($(SYSTEM),Windows)
EXP_CPPFLAGS += -DLUA_DL_DLOPEN
ifneq ($(SYSTEM),FreeBSD)
ifneq ($(SYSTEM),OpenBSD)
LUA_LDLIB:=-ldl
EXP_LDLIBS += -ldl
endif
endif
endif
ifneq ($(SYSTEM),Windows)
EXP_CPPFLAGS += -DLUA_USE_MKSTEMP
endif
ifeq ($(64bit),no)
ifeq ($(MACHINE),x86_64)
m32=yes
endif
BIT=32bit
else
ifeq ($(32bit),yes)
ifeq ($(MACHINE),x86_64)
m32=yes
endif
BIT=32bit
else
ifneq ($(MACHINE),x86_64)
m64=yes
endif
BIT=64bit
SPLINTD:=-D_LP64
endif
endif
ifeq ($(m32),yes)
GT_CFLAGS += -m32
GT_LDFLAGS += -m32
SQLITE_CFLAGS += -m32
endif
ifeq ($(m64),yes)
ifeq (,$(filter $(MACHINE),ia64 alpha mips64 mips64el aarch64))
GT_CFLAGS += -m64
GT_LDFLAGS += -m64
SQLITE_CFLAGS += -m64
endif
endif
ifeq ($(findstring clang,$(CC)),clang)
# do not complain about unnecessary options
GT_CFLAGS += -Qunused-arguments -Wno-parentheses -Wno-unknown-warning-option
GT_CPPFLAGS += -Qunused-arguments -Wno-parentheses -Wno-unknown-warning-option
# do not complain about indentation in 3rdparty code
GT_CFLAGS += -Wno-misleading-indentation
endif
# check whether version scripts can be used
ifneq ($(SYSTEM),Darwin)
ifeq ($(shell ld -V | grep GNU > /dev/null; echo $$?),0)
HAS_GNU_LD:=yes
VERSION_SCRIPT:=obj/public_symbols.lst
VERSION_SCRIPT_PARAM:=-Wl,--version-script=$(VERSION_SCRIPT)
else
HAS_GNU_LD:=no
endif
else
HAS_GNU_LD:=no
endif
ifneq ($(sharedlib),no)
SHARED_LIBGENOMETOOLS := lib/libgenometools$(SHARED_OBJ_NAME_EXT)
endif
ifeq ($(popcnt),yes)
ifeq ($(MACHINE),x86_64)
GT_CFLAGS += -mpopcnt
endif
endif
LIBGENOMETOOLS_DIRS:= src/core \
src/extended \
src/gtlua \
src/match \
src/ltr \
src/mgth
ifneq ($(cairo),no)
ifeq ($(SYSTEM),Darwin)
EXP_LDFLAGS:=
endif
ifeq ($(HAS_PKGCONFIG),yes)
GTSHAREDLIB_LIBDEP:= $(GTSHAREDLIB_LIBDEP) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --silence-errors --libs pango) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --silence-errors --libs cairo) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --silence-errors --libs pangocairo)
EXP_LDLIBS:=$(EXP_LDLIBS) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --silence-errors --libs pango) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --silence-errors --libs cairo) \
$(shell $(OVERRIDE_PC_PATH) pkg-config --silence-errors --libs pangocairo)
endif
ANNOTATIONSKETCH_EXAMPLES := bin/examples/sketch_constructed \
bin/examples/sketch_parsed_with_ctrack \
bin/examples/sketch_parsed_with_ordering \
bin/examples/sketch_parsed
ANNOTATIONSKETCH_MANUAL := doc/manuals/annotationsketch.pdf
LIBGENOMETOOLS_DIRS:=$(LIBGENOMETOOLS_DIRS) src/annotationsketch
SKETCH_EXTRA_BINARIES := bin/examples/sketch_parsed \
bin/examples/sketch_constructed
else
EXP_CPPFLAGS += -DWITHOUT_CAIRO
STEST_FLAGS += -nocairo
CAIRO_FILTER_OUT:=src/gtlua/annotationsketch_lua.c \
src/gtlua/canvas_lua.c \
src/gtlua/diagram_lua.c \
src/gtlua/image_info_lua.c \
src/gtlua/layout_lua.c
endif
ifneq ($(threads),no)
EXP_CPPFLAGS += -DGT_THREADS_ENABLED
EXP_LDLIBS += -lpthread
GTSHAREDLIB_LIBDEP += -lpthread
endif
ifneq ($(with-sqlite),no)
ifeq ($(useshared),yes)
EXP_LDLIBS += -lsqlite3
GTSHAREDLIB_LIBDEP += -lsqlite3
else
LIBGENOMETOOLS_DIRS := $(SQLITE3_DIR) $(LIBGENOMETOOLS_DIRS)
GT_CPPFLAGS += -I$(CURDIR)/$(SQLITE3_DIR)
OVERRIDELIBS += lib/libsqlite.a
ifeq ($(threads),yes)
EXP_CPPFLAGS += -DSQLITE_THREADSAFE=1
else
EXP_CPPFLAGS += -DSQLITE_THREADSAFE=0
endif
ifneq ($(SYSTEM),Windows)
EXP_LDLIBS += -lpthread
ifneq ($(SYSTEM),FreeBSD)
ifneq ($(SYSTEM),OpenBSD)
EXP_LDLIBS += -ldl
endif
endif
endif
endif
EXP_CPPFLAGS += -DHAVE_SQLITE
else
SQLITE_FILTER_OUT:=src/extended/rdb_sqlite.c
endif
ifeq ($(with-mysql),yes)
GTSHAREDLIB_LIBDEP:= $(GTSHAREDLIB_LIBDEP) -lmysqlclient
EXP_CPPFLAGS += -DHAVE_MYSQL
EXP_LDLIBS += -lmysqlclient
else
MYSQL_FILTER_OUT:=src/extended/rdb_mysql.c
ifeq ($(with-sqlite),no)
STEST_FLAGS += -nordb
endif
endif
# the GenomeTools library
LIBGENOMETOOLS_PRESRC:=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(sort $(wildcard $(DIR)/*.c)))
# remove AnnotationSketch-only bindings
LIBGENOMETOOLS_PRESRC:=$(filter-out $(CAIRO_FILTER_OUT),\
$(LIBGENOMETOOLS_PRESRC))
# remove MySQL-only files
LIBGENOMETOOLS_PRESRC:=$(filter-out $(MYSQL_FILTER_OUT),\
$(LIBGENOMETOOLS_PRESRC))
# remove SQLite-only files
LIBGENOMETOOLS_PRESRC:=$(filter-out $(SQLITE_FILTER_OUT),\
$(LIBGENOMETOOLS_PRESRC))
ifeq ($(amalgamation),yes)
# SQLite does not need to go into the amalgamation
LIBGENOMETOOLS_PRESRC:=$(filter-out $(SQLITE3_SRC),\
$(LIBGENOMETOOLS_PRESRC))
LIBGENOMETOOLS_SRC:=obj/amalgamation.c
GT_CFLAGS+=-Wno-strict-overflow
else
LIBGENOMETOOLS_SRC:=$(LIBGENOMETOOLS_PRESRC)
endif
LIBGENOMETOOLS_OBJ:=$(LIBGENOMETOOLS_SRC:%.c=obj/%.o)
LIBGENOMETOOLS_DEP:=$(LIBGENOMETOOLS_SRC:%.c=obj/%.d)
ifneq ($(useshared),yes)
LIBGENOMETOOLS_OBJ += $(LIBLUA_OBJ) \
$(SAMTOOLS_OBJ) \
$(LIBEXPAT_OBJ) \
$(LIBTRE_OBJ) \
$(LIBBZ2_OBJ) \
$(ZLIB_OBJ)
LIBGENOMETOOLS_DEP += $(LIBLUA_DEP) \
$(SAMTOOLS_DEP) \
$(LIBEXPAT_DEP) \
$(LIBTRE_DEP) \
$(LIBBZ2_DEP) \
$(ZLIB_DEP)
endif
ifneq ($(with-sqlite),no)
ifneq ($(useshared),yes)
LIBGENOMETOOLS_OBJ += lib/libsqlite.a
endif
endif
ifeq ($(wrapmemcpy),yes)
GT_LDFLAGS += -Wl,--wrap=memcpy
LIBGENOMETOOLS_OBJ += obj/src/memcpy.o
LUAMAIN_OBJ += obj/src/memcpy.o
endif
GT_CFLAGS_NO_WERROR:=$(GT_CFLAGS) -w
ifneq ($(errorcheck),no)
GT_CFLAGS += -Werror
endif
# set prefix for install target
prefix ?= /usr/local
ifdef DESTDIR
prefix:=$(DESTDIR)$(prefix)
endif
# allow to set patch program
patch ?= patch
ifneq ($(useshared),yes)
ADDITIONAL_BINARIES:=bin/lua
else
ADDITIONAL_BINARIES:=
endif
verbose ?= no
ifeq ($(verbose),no)
V_ECHO=@echo
V_DO=@
else
V_ECHO=@true
V_DO=
endif
all: lib/libgenometools.a $(SHARED_LIBGENOMETOOLS) \
bin/gt bin/examples/custom_stream \
bin/examples/gff3sort bin/examples/gff3validator bin/examples/noop \
$(ANNOTATIONSKETCH_EXAMPLES) \
$(ADDITIONAL_BINARIES)
.PHONY: go gotest
go: all
go install $(GOTAGS) -v ./gtgo/...
gotest: go
goimports -l -w gtgo
gofmt -l -w -s gtgo
golint gtgo
go vet github.com/genometools/genometools/gtgo
gff3validator_go testdata/encode_known_genes_Mar07.gff3
ifneq ($(cairo),no)
annotationsketch_demo_go testdata/encode_known_genes_Mar07.gff3 testdata/encode_known_genes_Mar07.png
endif
lib/libexpat.a: $(LIBEXPAT_OBJ)
$(V_ECHO) "[link $(@F)]"
$(V_DO)test -d $(@D) || mkdir -p $(@D)
$(V_DO)$(AR) ru $@ $(LIBEXPAT_OBJ)
ifdef RANLIB
$(V_DO)$(RANLIB) $@
endif
lib/libtre.a: $(LIBTRE_OBJ)
$(V_ECHO) "[link $(@F)]"
$(V_DO)test -d $(@D) || mkdir -p $(@D)
$(V_DO)$(AR) ru $@ $(LIBTRE_OBJ)
ifdef RANLIB
$(V_DO)$(RANLIB) $@
endif
lib/libsqlite.a: $(SQLITE3_OBJ)
$(V_ECHO) "[link $(@F)]"
$(V_DO)test -d $(@D) || mkdir -p $(@D)
$(V_DO)$(AR) ru $@ $(SQLITE3_OBJ)
ifdef RANLIB
$(V_DO)$(RANLIB) $@
endif
lib/libbz2.a: $(LIBBZ2_OBJ)
$(V_ECHO) "[link $(@F)]"
$(V_DO)test -d $(@D) || mkdir -p $(@D)
$(V_DO)$(AR) ru $@ $(LIBBZ2_OBJ)
ifdef RANLIB
$(V_DO)$(RANLIB) $@
endif
lib/libz.a: $(ZLIB_OBJ)
$(V_ECHO) "[link $(@F)]"
$(V_DO)test -d $(@D) || mkdir -p $(@D)
$(V_DO)$(AR) ru $@ $(ZLIB_OBJ)
ifdef RANLIB
$(V_DO)$(RANLIB) $@
endif
lib/libgenometools.a: obj/gt_config.h $(LIBGENOMETOOLS_OBJ)
$(V_ECHO) "[link $(@F)]"
$(V_DO)test -d $(@D) || mkdir -p $(@D)
$(V_DO)$(AR) r $@ $(LIBGENOMETOOLS_OBJ)
ifdef RANLIB
$(V_DO)$(RANLIB) $@
endif
ifneq ($(useshared),yes)
ADDITIONAL_ZLIBS:=lib/libbz2.a lib/libz.a
ADDITIONAL_SO_DEPS:=$(ADDITIONAL_ZLIBS) \
lib/libexpat.a
endif
lib/libgenometools$(SHARED_OBJ_NAME_EXT): obj/gt_config.h \
$(LIBGENOMETOOLS_OBJ) \
$(ADDITIONAL_SO_DEPS) \
$(ADDITIONAL_ZLIBS) \
$(VERSION_SCRIPT)
$(V_ECHO) "[link $(@F)]"
$(V_DO)test -d $(@D) || mkdir -p $(@D)
$(V_DO)$(CC) $(EXP_LDFLAGS) $(VERSION_SCRIPT_PARAM) \
$(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED) $(LIBGENOMETOOLS_OBJ) \
-o $@ $(GTSHAREDLIB_LIBDEP)
define PROGRAM_template
$(1): $(2)
$(V_ECHO) "[link $$(@F)]"
$(V_DO)test -d $$(@D) || mkdir -p $$(@D)
$(V_DO)$$(CC) $$(EXP_LDFLAGS) $$(GT_LDFLAGS) $$(filter-out $$(OVERRIDELIBS),$$^) \
$$(filter-out $$(patsubst lib%.a,-l%,$$(notdir $$(OVERRIDELIBS))),\
$$(EXP_LDLIBS)) $$(OVERRIDELIBS) $$(EXP_LDLIBS) -o $$@
endef
$(eval $(call PROGRAM_template, bin/gt, $(GTMAIN_OBJ) $(TOOLS_OBJ) \
lib/libgenometools.a \
$(ADDITIONAL_ZLIBS)))
$(eval $(call PROGRAM_template, bin/examples/custom_stream, \
obj/src/examples/custom_stream.o \
lib/libgenometools.a\
$(ADDITIONAL_ZLIBS)))
$(eval $(call PROGRAM_template, bin/examples/gff3sort, \
obj/src/examples/gff3sort.o \
lib/libgenometools.a \
$(ADDITIONAL_ZLIBS)))
$(eval $(call PROGRAM_template, bin/examples/gff3validator, \
obj/src/examples/gff3validator.o \
lib/libgenometools.a \
$(ADDITIONAL_ZLIBS)))
$(eval $(call PROGRAM_template, bin/examples/noop, \
obj/src/examples/noop.o \
lib/libgenometools.a \
$(ADDITIONAL_ZLIBS)))
$(eval $(call PROGRAM_template, bin/examples/sketch_constructed, \
obj/src/examples/sketch_constructed.o \
lib/libgenometools.a \
$(ADDITIONAL_ZLIBS)))
$(eval $(call PROGRAM_template, bin/examples/sketch_parsed, \
obj/src/examples/sketch_parsed.o \
lib/libgenometools.a \
$(ADDITIONAL_ZLIBS)))
$(eval $(call PROGRAM_template, bin/examples/sketch_parsed_with_ctrack, \
obj/src/examples/sketch_parsed_with_ctrack.o \
lib/libgenometools.a \
$(ADDITIONAL_ZLIBS)))
$(eval $(call PROGRAM_template, bin/examples/sketch_parsed_with_ordering, \
obj/src/examples/sketch_parsed_with_ordering.o \
lib/libgenometools.a \
$(ADDITIONAL_ZLIBS)))
bin/lua: $(LUAMAIN_OBJ)
$(V_ECHO) "[link $(@F)]"
$(V_DO)test -d $(@D) || mkdir -p $(@D)
$(V_DO)$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $^ -lm $(LUA_LDLIB) -o $@
API_HEADERS=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(sort $(wildcard $(DIR)/*_api.h)))
obj/public_symbols.lst: $(API_HEADERS) $(LIBGENOMETOOLS_SRC)
$(V_DO)echo '[gathering public API symbols to $@]'
$(V_DO)printf "VERSION {\n\tglobal:\n" > $@
$(V_DO)cat $(API_HEADERS) | tr ' ' '\n' \
| grep -E '^(gt_[0-9a-zA-Z_]+)(\[|\()' \
| cut -d'[' -f1 | cut -d'(' -f1 | sort | uniq > [email protected]
$(V_DO)cat $(LIBGENOMETOOLS_PRESRC) | tr ' ' '\n' \
| grep -E '(gt_[0-9a-zA-Z_]+_p)(\[|\()' \
| cut -d'(' -f1 >> [email protected]
$(V_DO)for L in `cat [email protected]`; do \
printf "\t\t$$L;\n" >> $@; \
done;
$(V_DO)printf "\t\tgt_array_add_ptr;\n" >> $@
$(V_DO)printf "\t\tgt_str_get_mem;\n" >> $@
$(V_DO)printf '\tlocal: *;\n\t};\n' >> $@
obj/gt_config.h: VERSION
$(V_DO)echo '[create $@]'
$(V_DO)test -d $(@D) || mkdir -p $(@D)
$(V_DO)(echo '#ifndef GT_CONFIG_H' ;\
echo '#define GT_CONFIG_H' ;\
echo '#define GT_CC "'`$(CC) --version | head -n 1`\" ;\
echo '#define GT_CFLAGS "$(EXP_CFLAGS) $(GT_CFLAGS)"' ;\
echo '$(EXP_CPPFLAGS) $(GT_CPPFLAGS)' | \
sed -e 's/\([^\]\)"/\1\\"/g' -e 's/^"/\\"/g' -e 's/$$/"/' \
-e 's/^/#define GT_CPPFLAGS "/'; \
echo '#define GT_VERSION "'`cat VERSION`\" ) > $@
$(V_DO)cat VERSION | \
sed 's/\([0-9]*\)\.[0-9]*\.[0-9]*/#define GT_MAJOR_VERSION \1/' >> $@
$(V_DO)cat VERSION | \
sed 's/[0-9]*\.\([0-9]*\)\.[0-9]*/#define GT_MINOR_VERSION \1/' >> $@
$(V_DO)cat VERSION | \
sed 's/[0-9]*\.[0-9]*\.\([0-9]*\)/#define GT_MICRO_VERSION \1/' >> $@
$(V_DO)echo '#endif' >> $@
obj/amalgamation.c: $(LIBGENOMETOOLS_PRESRC)
$(V_ECHO) '[create $@]'
$(V_DO)test -d $(@D) || mkdir -p $(@D)
$(V_DO)scripts/create_amalgamation $(LIBGENOMETOOLS_PRESRC) > $@
bitpackstringop_Dependencies=src/core/bitpackstringop.template \
src/core/bitpackstringvectorreadop.gen \
src/core/bitpackstringvectorwriteop.gen \
scripts/template2c.pl
src/core/bitpackstringop8.c: $(bitpackstringop_Dependencies)
$(V_ECHO) '[rebuild $@]'
$(V_DO)scripts/template2c.pl 8 $<
src/core/checkbitpackstring8.c: \
src/core/checkbitpackstring.template scripts/template2c.pl
$(V_ECHO) '[rebuild $@]'
$(V_DO)scripts/template2c.pl 8 $<
src/core/bitpackstringop16.c: $(bitpackstringop_Dependencies)
$(V_ECHO) '[rebuild $@]'
$(V_DO)scripts/template2c.pl 16 $<
src/core/checkbitpackstring16.c: \
src/core/checkbitpackstring.template scripts/template2c.pl
$(V_ECHO) '[rebuild $@]'
$(V_DO)scripts/template2c.pl 16 $<
src/core/bitpackstringop32.c: $(bitpackstringop_Dependencies)
$(V_ECHO) '[rebuild $@]'
$(V_DO)scripts/template2c.pl 32 $<
src/core/checkbitpackstring32.c: \
src/core/checkbitpackstring.template scripts/template2c.pl
$(V_ECHO) '[rebuild $@]'
$(V_DO)scripts/template2c.pl 32 $<
src/core/bitpackstringop64.c: $(bitpackstringop_Dependencies)
$(V_ECHO) '[rebuild $@]'
$(V_DO)scripts/template2c.pl 64 $<
src/core/checkbitpackstring64.c: \
src/core/checkbitpackstring.template scripts/template2c.pl
$(V_ECHO) '[rebuild $@]'
$(V_DO)scripts/template2c.pl 64 $<
src/core/checkbitpackstring-int.c: \
src/core/checkbitpackstring.template scripts/template2c.pl
$(V_ECHO) '[rebuild $@]'
$(V_DO)scripts/template2c.pl '-int' $<
src/extended/intset_8.c src/extended/intset_8.h src/extended/intset_16.c \
src/extended/intset_16.h src/extended/intset_32.c src/extended/intset_32.h: \
./scripts/gen-intsets.rb
$(V_ECHO) '[rebuild] $@'
$(V_DO)$<
# SQLite needs special attention
obj/$(SQLITE3_DIR)/%.o: $(SQLITE3_DIR)/%.c
$(V_ECHO) "[compile $(@F)]"
$(V_DO)test -d $(@D) || mkdir -p $(@D)
$(V_DO)$(CC) -c $< -o $@ -DHAVE_MALLOC_USABLE_SIZE $(EXP_CPPFLAGS) \
$(GT_CPPFLAGS) $(EXP_CFLAGS) $(SQLITE_CFLAGS) -DSQLITE_ENABLE_UNLOCK_NOTIFY $(FPIC)
$(V_DO)$(CC) -c $< -o $(@:.o=.d) -DHAVE_MALLOC_USABLE_SIZE $(EXP_CPPFLAGS) \
$(GT_CPPFLAGS) -MM -MP -MT $@ $(FPIC)
# TRE needs special attention
obj/$(TRE_DIR)/%.o: $(TRE_DIR)/%.c
$(V_ECHO) "[compile $(@F)]"
$(V_DO)test -d $(@D) || mkdir -p $(@D)
$(V_DO)$(CC) -c $< -o $@ $(EXP_CPPFLAGS) \
$(GT_CPPFLAGS) $(EXP_CFLAGS) $(TRE_CPPFLAGS) $(GT_CFLAGS) -Wno-int-in-bool-context $(FPIC)
$(V_DO)$(CC) -c $< -o $(@:.o=.d) $(EXP_CPPFLAGS) \
$(GT_CPPFLAGS) $(TRE_CPPFLAGS) -MM -MP -MT $@ $(FPIC)
define COMPILE_template
$(1): $(2)
$(V_ECHO) "[compile $$(@F)]"
$(V_DO)test -d $$(@D) || mkdir -p $$(@D)
$(V_DO)$$(CC) -c $$< -o $$@ $$(EXP_CPPFLAGS) $$(GT_CPPFLAGS) $$(EXP_CFLAGS) \
$$(GT_CFLAGS) $(3)
$(V_DO)$$(CC) -c $$< -o $$(@:.o=.d) $$(EXP_CPPFLAGS) $$(GT_CPPFLAGS) $$(EXP_CFLAGS) \
$(3) -MM -MP -MT $$@
endef
obj/$(SAMTOOLS_DIR)/%.o: $(SAMTOOLS_DIR)/%.c
$(V_ECHO) "[compile $(notdir $@)]"
$(V_DO)test -d $(@D) || mkdir -p $(@D)
$(V_DO)$(CC) -c $< -o $@ $(EXP_CPPFLAGS) $(GT_CPPFLAGS) \
$(EXP_CFLAGS) $(GT_CFLAGS_NO_WERROR)
$(V_DO)$(CC) -c $< -o $(@:.o=.d) $(EXP_CPPFLAGS) $(GT_CPPFLAGS) -MM -MP \
-MT $@
$(eval $(call COMPILE_template, obj/%.o, %.c))
obj/%.o: %.cxx
$(V_ECHO) "[compile $@]"
$(V_DO)test -d $(@D) || mkdir -p $(@D)
$(V_DO)$(CXX) -c $< -o $@ $(EXP_CPPFLAGS) $(GT_CPPFLAGS) \
$(EXP_CXXFLAGS) $(GT_CXXFLAGS)
$(V_DO)$(CXX) -c $< -o $(@:.o=.d) $(EXP_CPPFLAGS) $(GT_CPPFLAGS) -MM -MP \
-MT $@
obj/%.o: %.cpp
$(V_ECHO) "[compile $@]"
$(V_DO)test -d $(@D) || mkdir -p $(@D)
$(V_DO)$(CXX) -c $< -o $@ $(EXP_CPPFLAGS) $(GT_CPPFLAGS) \
$(EXP_CXXFLAGS) $(GT_CXXFLAGS)
$(V_DO)$(CXX) -c $< -o $(@:.o=.d) $(EXP_CPPFLAGS) $(GT_CPPFLAGS) -MM -MP \
-MT $@
obj/src/core/versionfunc.o: obj/gt_config.h
# read dependencies
-include $(GTMAIN_DEP) \
$(EXAMPLES_DEP) \
$(TOOLS_DEP) \
$(LUAMAIN_DEP) \
$(LIBBZ2_DEP) \
$(ZLIB_DEP) \
$(SAMTOOLS_DEP) \
$(LIBGENOMETOOLS_DEP) \
obj/src/examples/custom_stream.d \
obj/src/examples/gff3sort.d \
obj/src/examples/gff3validator.d \
obj/src/examples/noop.d \
obj/src/examples/sketch_constructed.d \
obj/src/examples/sketch_parsed.d
.PRECIOUS:
.SUFFIXES:
.PHONY: dist srcdist release gt install docs manuals installwww push \
test clean cleanup
VERSION:="`cat $(CURDIR)/VERSION`"
SYSTEMNAME:="$(SYSTEM)_$(MACHINE)"
GTDISTBASENAME:="gt-$(VERSION)-$(SYSTEMNAME)-$(BIT)$(DISTSUFFIX)"
DISTDIR:="$(CURDIR)/dist/$(SYSTEMNAME)"
SCRIPTSDIR:="$(CURDIR)/scripts"
GTDISTDIR:="$(DISTDIR)/$(GTDISTBASENAME)"
STRIP:=strip
dist: all
$(V_ECHO) "[build distribution]"
$(V_DO)rm -rf $(GTDISTDIR)
ifeq ($(SYSTEM),Windows)
$(V_DO)rm -f $(DISTDIR)/$(GTDISTBASENAME).zip
else
$(V_DO)rm -f $(DISTDIR)/$(GTDISTBASENAME).tar.gz
endif
$(V_DO)mkdir -p $(GTDISTDIR)/bin $(GTDISTDIR)/doc
$(V_DO)cp $(CURDIR)/doc/dist_readme.txt $(GTDISTDIR)/README
$(V_DO)cp $(CURDIR)/LICENSE $(GTDISTDIR)
$(V_DO)cp $(CURDIR)/CONTRIBUTORS $(GTDISTDIR)
$(V_DO)cp $(CURDIR)/CHANGELOG $(GTDISTDIR)
$(V_DO)cp $(CURDIR)/doc/manuals/*.pdf $(GTDISTDIR)/doc
$(V_DO)cp -r $(CURDIR)/gtdata $(GTDISTDIR)
$(V_DO)cp -r $(CURDIR)/gtpython $(GTDISTDIR)
$(V_DO)cp -r $(CURDIR)/gtruby $(GTDISTDIR)
$(V_DO)$(MAKE) prefix=$(GTDISTDIR) install
ifeq ($(SYSTEM),Windows)
$(V_DO)cd $(DISTDIR) && 7z a -tzip $(GTDISTBASENAME).zip $(GTDISTBASENAME)
$(V_ECHO) "$(DISTDIR)/$(GTDISTBASENAME).zip"
else
$(V_DO)cd $(DISTDIR) && $(SCRIPTSDIR)/tar_root.sh $(GTDISTBASENAME)
$(V_DO)cd $(DISTDIR) && gzip -f -9 $(GTDISTBASENAME).tar
$(V_ECHO) "$(DISTDIR)/$(GTDISTBASENAME).tar.gz"
endif
srcdist:
git archive --format=tar --prefix=genometools-`cat VERSION`/ HEAD | \
gzip -9 > genometools-`cat VERSION`.tar.gz
release:
git tag "v`cat VERSION`"
git archive --format=tar --prefix="genometools-`cat VERSION`"/ HEAD | \
gzip -9 > genometools-`cat VERSION`.tar.gz
scp "genometools-`cat VERSION`.tar.gz" $(SERVER):$(WWWBASEDIR)/genometools.org/htdocs/pub
git push --tags origin master
git push --tags github master
docs: bin/gt $(SKETCH_EXTRA_BINARIES)
bin/gt gtscripts/gtdoc.lua -html $(CURDIR) \
> www/genometools.org/htdocs/libgenometools.html
bin/gt gtscripts/gtdoc.lua -lua -html $(CURDIR) \
> www/genometools.org/htdocs/docs.html
ifdef SKETCH_EXTRA_BINARIES
bin/examples/sketch_parsed gtdata/sketch/default.style \
www/genometools.org/htdocs/images/parsed.png \
testdata/eden.gff3
bin/examples/sketch_parsed \
www/genometools.org/htdocs/annotationsketch/callbacks.style \
www/genometools.org/htdocs/images/callbacks.png \
www/genometools.org/htdocs/annotationsketch/callback_examples_with_score.gff3
bin/examples/sketch_constructed gtdata/sketch/default.style \
www/genometools.org/htdocs/images/constructed.png
endif
sed -nf scripts/incl.sed \
www/genometools.org/htdocs/examples_tmpl.html | \
sed 'N;N;s/\n//' > /tmp/tmp.sed.$$$$ && \
sed -f /tmp/tmp.sed.$$$$ \
www/genometools.org/htdocs/examples_tmpl.html > \
www/genometools.org/htdocs/examples.html; rm -f /tmp/tmp.sed.$$$$
bin/gt gtscripts/gtdoc.lua -tex $(CURDIR) \
> doc/manuals/api_reference.tex
bin/gt gtscripts/gtdoc.lua -lua -tex $(CURDIR) \
> doc/manuals/gtscript_reference.tex
$(MAKE) -C $(CURDIR)/doc/devguide
bin/gt -list > /tmp/list.txt
bin/gt -createman /tmp/gtmanpages
asciidoc --backend=xhtml11 -a linkcss -a stylesdir=. \
-a stylesheet=style.css -a badges -a icons \
-f www/genometools.org/htdocs/tool_list.conf \
--out-file www/genometools.org/htdocs/tools.html /tmp/list.txt
test -d www/genometools.org/htdocs/tools || mkdir -p www/genometools.org/htdocs/tools
rm -f www/genometools.org/htdocs/tools/*
scripts/create_html /tmp/gtmanpages www/genometools.org/htdocs/
rm -rf /tmp/list.txt /tmp/gtmanpages
doc/manuals/annotationsketch.pdf: docs
$(MAKE) -C $(CURDIR)/doc/manuals annotationsketch
manuals: bin/gt $(ANNOTATIONSKETCH_MANUAL)
$(MAKE) -C $(CURDIR)/doc/manuals
manpages: bin/gt
bin/gt -createman /tmp/gtmanpages
test -d $(CURDIR)/doc/manpages || mkdir -p $(CURDIR)/doc/manpages
rm -f $(CURDIR)/doc/manpages/*
scripts/create_manpages /tmp/gtmanpages $(CURDIR)/doc/manpages
installwww:
# install genometools.org website
rsync -rv www/genometools.org/ $(SERVER):$(WWWBASEDIR)/genometools.org
push:
git push origin master
git push github master
gt: bin/gt
install: all
test -d $(prefix)/bin || mkdir -p $(prefix)/bin
ifeq ($(SYSTEM),Windows)
cp bin/gt $(prefix)/bin/gt.exe
$(STRIP) $(prefix)/bin/gt.exe
else
cp bin/gt $(prefix)/bin
$(STRIP) $(prefix)/bin/gt
endif
mkdir -p $(prefix)/share/genometools
cp -a gtdata $(prefix)/share/genometools/