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Makefile
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SHELL=/bin/sh
BUILDER_VERSION= $(shell sed -e '/Id/!d' -e 's/[^0-9.]*\([0-9.]*\).*/\1/' -e q Makefile )
version:
# +-------------------------------------+
# | QUARANTINE BUILDER VERSION: ${BUILDER_VERSION} |
# +-------------------------------------+
@echo
@echo "Syntax: make [option]"
@echo "Useful options are:"
@echo " untar - get packages from web and untar"
@echo " utils - util libs (perl, PMP, etc)"
@echo " mnilibs - internal BIC libs (bicpl, EBTKS, etc)"
@echo " main - core codes (pve, clasp, surfreg, etc)"
@echo " civet - CIVET pipeline (internal, development)"
@echo " visual - BIC viewers (Display, register, brainview)"
@echo " clean - clean-up (incomplete)"
@echo " imagemagick - from ftp://ftp.imagemagick.org/pub/"
@echo
@echo "If some modules fail to compile, you may have to install"
@echo "the following packages on your Linux Debian/Ubuntu system:"
@echo " sudo apt-get install build-essential "
@echo " libx11-dev freeglut3-dev libgmp3-dev libgnome-perl"
@echo " gawk zlib1g-dev m4 libgnome2-dev libgnome-dev xlibs-dev"
@echo " r-base r-base-core r-base-dev"
@echo "For verify images, adding the following:"
@echo " imagemagick"
@echo "or install it from sources at ftp://ftp.imagemagick.org/pub/"
@echo
@echo "On CentOS, modules to install are:"
@echo " sudo yum groupinstall 'Development Tools'"
@echo " sudo yum install zlib-devel"
@echo " sudo yum install libjpeg-devel"
@echo " sudo yum install libpng-devel"
@echo " sudo yum install libtiff-devel"
@echo " sudo yum install lcms2-devel"
@echo " sudo yum install which"
@echo " sudo yum install cpan"
@echo " cpan install ExtUtils::MakeMaker"
@echo " sudo yum install libX11-devel"
@echo " sudo yum install freeglut-devel"
@echo " sudo yum install perl-Env"
@echo " sudo yum install perl-Perl4-CoreLibs"
@echo " sudo yum install gnuplot"
@echo
@echo "For Ubuntu 16.0/18.0:"
@echo " sudo apt-get install libz-dev libjpeg-dev libpng-dev "
@echo " libtiff-dev liblcms2-dev flex libx11-dev freeglut3-dev "
@echo " libxmu-dev libxi-dev libqt4-dev "
@echo " sudo apt-get install libfreetype6-dev "
@echo " for fonts on png before compiling ImageMagick"
@echo
@echo "Copyright Alan C. Evans"
@echo "Professor of Neurology"
@echo "McGill University"
@echo
packages:
@echo
@echo "Creating civet$(CIVET_VERS)-cdrom.tar.gz from TGZ..."
@echo
mkdir -p dist
mkdir -p dist/TGZ
@cp -f -p Makefile dist/
@cp -f -p mk_environment.pl dist/
@cp -f -p install.sh dist/
@cp -f -p LICENSE dist/
@cp -f -p $(ADNI_TAR) dist/TGZ/
@cp -f -p $(ARGS_TAR) dist/TGZ/
@cp -f -p $(AUTOREG_TAR) dist/TGZ/
@cp -f -p $(AVG305_TAR) dist/TGZ/
@cp -f -p $(BET_TAR) dist/TGZ/
@cp -f -p $(BICINVENTOR_TAR) dist/TGZ/
@cp -f -p $(BOOST_TAR) dist/TGZ/
@cp -f -p $(BICPL_TAR) dist/TGZ/
@cp -f -p $(BRAINVIEW_TAR) dist/TGZ/
@cp -f -p $(CAREA_TAR) dist/TGZ/
@cp -f -p $(NETCDF_TAR) dist/TGZ/
@cp -f -p $(CGAL_TAR) dist/TGZ/
@cp -f -p $(CIVET_TAR) dist/TGZ/
@cp -f -p $(CLASP_TAR) dist/TGZ/
@cp -f -p $(CLASSIFY_TAR) dist/TGZ/
@cp -f -p $(COIN_TAR) dist/TGZ/
@cp -f -p $(COLIN27_TAR) dist/TGZ/
@cp -f -p $(CONGLOMERATE_TAR) dist/TGZ/
@cp -f -p $(CSURFACE_TAR) dist/TGZ/
@cp -f -p $(DISPLAY_TAR) dist/TGZ/
@cp -f -p $(EBTKS_TAR) dist/TGZ/
@cp -f -p $(GETOPT_TAR) dist/TGZ/
@cp -f -p $(GGS_TAR) dist/TGZ/
@cp -f -p $(GSL_TAR) dist/TGZ/
@cp -f -p $(HDF_TAR) dist/TGZ/
@cp -f -p $(ICBM152_TAR) dist/TGZ/
@cp -f -p $(ICBM152NL_TAR) dist/TGZ/
@cp -f -p $(ICBM152NL09_TAR) dist/TGZ/
@cp -f -p $(ICBMTEMP_TAR) dist/TGZ/
@cp -f -p $(ILT_TAR) dist/TGZ/
@cp -f -p $(IMAGEMAGICK_TAR) dist/TGZ/
@cp -f -p $(INORM_TAR) dist/TGZ/
@cp -f -p $(LOBESEG_TAR) dist/TGZ/
@cp -f -p $(LAPLACE_TAR) dist/TGZ/
@cp -f -p $(M4_TAR) dist/TGZ/
@cp -f -p $(MINC_TAR) dist/TGZ/
@cp -f -p $(MRISIM_TAR) dist/TGZ/
@cp -f -p $(N3_TAR) dist/TGZ/
@cp -f -p $(NETPBM_TAR) dist/TGZ/
@cp -f -p $(OOBICPL_TAR) dist/TGZ/
@cp -f -p $(PCREPP_TAR) dist/TGZ/
@cp -f -p $(PCRE_TAR) dist/TGZ/
@cp -f -p $(PERLLIB_TAR) dist/TGZ/
@cp -f -p $(PMP_TAR) dist/TGZ/
@cp -f -p $(PVE_TAR) dist/TGZ/
@cp -f -p $(RAY_TRACE_TAR) dist/TGZ/
@cp -f -p $(REGISTER_TAR) dist/TGZ/
@cp -f -p $(SIMAGE_TAR) dist/TGZ/
@cp -f -p $(SOQT_TAR) dist/TGZ/
@cp -f -p $(STXSEG_TAR) dist/TGZ/
@cp -f -p $(SURFREG_TAR) dist/TGZ/
@cp -f -p $(TRUEFONT_TAR) dist/TGZ/
mkdir -p dist/Test
@cp -f -p Test/mni_icbm_00100_t1.mnc dist/Test/
cd dist; \
tar cvf civet$(CIVET_VERS)-cdrom.tar * ; \
gzip civet$(CIVET_VERS)-cdrom.tar ; \
mv civet$(CIVET_VERS)-cdrom.tar.gz .. ; \
cd ..; \
rm -rf dist
@echo
@echo "...done"
@echo
source_packages:
@echo
@echo "Creating civet$(CIVET_VERS)-cdrom.tar.gz from sources..."
@echo
mkdir -p dist
mkdir -p dist/TGZ
@cp -f -p Makefile dist/
@cp -f -p mk_environment.pl dist/
@cp -f -p install.sh dist/
@cp -f -p LICENSE dist/
for pkg in ${ADNI_PACKAGE} \
${ARGS_PACKAGE} \
${AUTOREG_PACKAGE} \
${AVG305_PACKAGE} \
${BET_PACKAGE} \
${BICPL_PACKAGE} \
${CAREA_PACKAGE} \
${CIVET_PACKAGE} \
${CLASP_PACKAGE} \
${CLASSIFY_PACKAGE} \
${COLIN27_PACKAGE} \
${CONGLOMERATE_PACKAGE} \
${CSURFACE_PACKAGE} \
${EBTKS_PACKAGE} \
${GETOPT_PACKAGE} \
${ICBM152_PACKAGE} \
${ICBM152NL_PACKAGE} \
${ICBM152NL09_PACKAGE} \
${ICBMTEMP_PACKAGE} \
${ILT_PACKAGE} \
${INORM_PACKAGE} \
${LAPLACE_PACKAGE} \
${MINC_PACKAGE} \
${N3_PACKAGE} \
${OOBICPL_PACKAGE} \
${PERLLIB_PACKAGE} \
${PMP_PACKAGE} \
${SURFREG_PACKAGE} \
${RAY_TRACE_PACKAGE} ; do \
cd ${SOURCE_DIR}/$$pkg/ ; \
make dist ; cd - ; \
mv -f ${SOURCE_DIR}/$$pkg/$$pkg.tar.gz dist/TGZ/ ; \
done
if [ ! -e ${SOURCE_DIR}/${PVE_PACKAGE}/configure ] ; then \
cd ${SOURCE_DIR}/${PVE_PACKAGE}/src ; \
make dist ; cd - ; \
mv -f ${SOURCE_DIR}/${PVE_PACKAGE}/src/${PVE_PACKAGE}.tar.gz dist/TGZ/ ; \
else \
cd ${SOURCE_DIR}/${PVE_PACKAGE}/ ; \
make dist ; cd - ; \
mv -f ${SOURCE_DIR}/${PVE_PACKAGE}/${PVE_PACKAGE}.tar.gz dist/TGZ/ ; \
fi
cd ${SOURCE_DIR}/ ; \
tar --exclude='*/.git' --exclude='*/CVS' -cvf ${M4_PACKAGE}.tar m4 ; \
gzip ${M4_PACKAGE}.tar ; \
cd - ; \
mv -f ${SOURCE_DIR}/${M4_PACKAGE}.tar.gz dist/TGZ/
for pkg in ${BOOST_TAR} \
${NETCDF_TAR} \
${CGAL_TAR} \
${GSL_TAR} \
${HDF_TAR} \
${NETPBM_TAR} \
${PCREPP_TAR} \
${PCRE_TAR} ; do \
cp -f -p $$pkg dist/TGZ/ ; \
done
mkdir -p dist/Test
@cp -f -p Test/mni_icbm_00100_t1.mnc dist/Test/
cd dist; \
tar cvf civet$(CIVET_VERS)-cdrom.tar * ; \
gzip civet$(CIVET_VERS)-cdrom.tar ; \
mv civet$(CIVET_VERS)-cdrom.tar.gz .. ; \
cd ..; \
rm -rf dist
@echo
@echo "...done"
@echo
binaries:
@echo
@echo "Packaging binaries for civet$(CIVET_VERS)-binaries.tar.gz..."
@echo
tar --exclude='$(UNAME)/share/hdf5_examples' \
-cvf civet$(CIVET_VERS)-binaries.tar $(UNAME)/bin \
$(UNAME)/CIVET$(CIVET_VERS) $(UNAME)/doc \
$(UNAME)/etc $(UNAME)/lib $(UNAME)/perl \
$(UNAME)/init.* $(UNAME)/share \
job_test Test/mni_icbm_00100_t1.mnc \
LICENSE
gzip civet$(CIVET_VERS)-binaries.tar
@echo
@echo "...done"
@echo
.PHONY: clean clean_dist
# +-------------------------+
# | SET SOME DEFAULTS |
# +-------------------------+
GTAR=tar
GTAR_FLAGS=-xzf
ABI = 64
DEBUG = 0
STATIC = 0
UNAME = $(shell uname)-$(shell uname -m | sed 's/ /_/g')
SOURCE_DIR = $(PWD)/$(UNAME)/SRC
PREFIX_PATH = $(PWD)/$(UNAME)
BUILD_PATH = $(PREFIX_PATH)
R_LIBS = $(PREFIX_PATH)/R_LIBS
MATLAB_ROOT = /usr/local/matlab
ANIMAL = no
MRI_SIM = no
MAGICK = no
USE_CVS = no
USE_GIT = no
QUARANTINE_FLAG = $(PWD)/$(UNAME)/.quarantine_created
LDFLAGS := -L$(PREFIX_PATH)/lib
PATH := $(PREFIX_PATH)/bin:$(PATH)
LD_LIBRARY_PATH := $(PREFIX_PATH)/lib:$(LD_LIBRARY_PATH)
OPT_OPTIONS :=
# +---------------------------------------------------+
# | STATIC OR DYNAMIC COMPILATION FOR BIC LIBRARIES |
# +---------------------------------------------------+
### fix LIB_EXT for cygwin and os-x (dll, dylib, whatever)
ifeq ($(STATIC),1)
BIC_STATIC = --enable-shared=no --enable-static=yes
LIB_EXT = a
else
BIC_STATIC = --enable-shared=yes --enable-static=no
LIB_EXT = so
ifneq ($(findstring Darwin,$(shell uname)),)
LIB_EXT = dylib
endif
endif
# +-------------------------------------+
# | OPTIMIZATION LEVEL (defaut opt) |
# +-------------------------------------+
ifeq ($(DEBUG),1)
OPT_OPTIONS += -g
else
ifneq ($(findstring IRIX,$(shell uname)),)
OPT_OPTIONS += -g -O2
else
ifneq ($(findstring Linux,$(shell uname)),)
ifneq ($(findstring ia64,$(shell uname -m)),)
OPT_OPTIONS += -g -O1
else
OPT_OPTIONS += -g -O2
endif
else
OPT_OPTIONS += -g -O2
endif
endif
endif
# These options are needed to compile with new gcc compilers (like 4.6 and above)
# (See http://www.amigacoding.de/index.php?topic=301.0).
GCCVERSIONSTRING=$(shell gcc -dumpversion)
empty:=
space:= $(empty) $(empty)
GCCVERSION := $(shell expr `echo $(GCCVERSIONSTRING)` | cut -f1 -d.)
GCCVERSION += $(shell expr `echo $(GCCVERSIONSTRING)` | cut -f2 -d.)
GCCVERSION += $(shell expr `echo $(GCCVERSIONSTRING)` | cut -f3 -d.)
# Make sure the version number has at least 3 decimals
GCCVERSION += 00
# Remove spaces from the version number
GCCVERSION := $(subst $(space),$(empty),$(GCCVERSION))
# Crop the version number to 3 decimals.
GCCVERSION := $(shell expr `echo $(GCCVERSION)` | cut -b1-3)
ifeq ($(shell expr `echo $(GCCVERSION)` \>= 460), 1)
$(info new compiler $(GCCVERSION))
OPT_OPTIONS += -D_GNU_SOURCE
CFLAGS=${OPT_OPTIONS} -std=c99
CPPFLAGS=${OPT_OPTIONS}
CXXFLAGS=${OPT_OPTIONS} -Wno-comment -Wno-write-strings
ifeq ($(shell expr `echo $(GCCVERSION)` \>= 470), 1)
CXXFLAGS+= -Wno-unused-local-typedefs
endif
### LDFLAGS:='-Wl,--no-as-needed ${LDFLAGS}'
LDFLAGS :='-Wl,--no-as-needed ${LDFLAGS}'
BRAINVIEWLDFLAGS :='-Wl,--no-as-needed -L$(PREFIX_PATH)/lib -L/usr/lib64/ -lQt3Support'
else
$(info old compiler $(GCCVERSION))
CFLAGS=${OPT_OPTIONS}
CPPFLAGS=${OPT_OPTIONS}
CXXFLAGS=${OPT_OPTIONS}
endif
# +----------------------------------+
# | SET ARCH and OS specific bits |
# +----------------------------------+
# +---------- IRIX64 ----------------+
ifneq ($(findstring IRIX,$(shell uname)),)
JAMARCH=bin.irixmips
BICPL_BUILD_SWITCH=--with-image-sgi
CPPFLAGS+=-I$(PREFIX_PATH)/include -I$(PREFIX_PATH)/include/volume_io -I/usr/include/gl
# THESE ARE BIC SPECIFIC THINGS
PERL=$(shell which /usr/local/perl5.8/bin/perl5.8.5)
GTAR:=gtar
else
PERL=$(shell which perl)
endif
# +---------- Linux ----------------+
ifneq ($(findstring Linux,$(shell uname)),)
BICPL_BUILD_SWITCH=--with-image-netpbm
ifneq ($(findstring x86_64,$(shell uname -m)),)
JAMARCH=bin.linuxx86_64
# some silliness for RMINC-0.4 on Linux 64 bits
CFLAGS+=-fpic
CPPFLAGS+=-fpic
CXXFLAGS+=-fpic
MEX_EXT=mexa64
else
JAMARCH=bin.linuxx86
MEX_EXT=mexglx
endif
ifneq ($(findstring ia64,$(shell uname -m)),)
JAMARCH=bin.linuxia64
endif
endif
# +----------- Darwin ----------------+
ifneq ($(findstring Darwin,$(shell uname)),)
BICPL_BUILD_SWITCH=--with-image-netpbm
ifneq ($(findstring i386,$(shell uname -m)),)
JAMARCH=bin.macosxx86
else
JAMARCH=bin.macosxppc
endif
BUILD_PATH := $(BUILD_PATH)/:/sw
DYLD_LIBRARY_PATH=$(PREFIX_PATH)/lib
VIEWER_OPTS='--with-apple-opengl-framework'
## add dylib for MAC to avoid recycle
VIEWER_LDFLAGS=${LDFLAGS} -L/Applications/MNI/Darwin-i386//lib -dylib_file \
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:\
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
else
VIEWER_OPTS='--with-x'
VIEWER_LDFLAGS=-L$(PREFIX_PATH)/lib
endif
CFG_COMP_FLAGS=CFLAGS='${CFLAGS}' CPPFLAGS='${CPPFLAGS}' CXXFLAGS='${CXXFLAGS}'
# +-----------------------------------------------+
# | SET MINC BASE VERSION (MUST BE 2) |
# +-----------------------------------------------+
MINC_BASE=2
MINC_COMPRESS=4
MINC_FORCE_V2=1
MINC_EXTRA = $(BIC_STATIC) --enable-acr-nema --enable-minc2
MINC_FLAG = --with-minc2
# +-------------------------------------------+
# | SET VERSION NUMBERS, PACKAGE NAMES, ETC |
# +-------------------------------------------+
ADNI_VERS=-1.2
ADNI_PACKAGE=mni-models_adni_nl${ADNI_VERS}
ADNI_GIT=git@github.com:aces/mni-models_adni_nl.git
ADNI_GIT_TAG=mni_adni_nl_1-2
ADNI_CVS=mni-models/adni-nl
ADNI_CVS_TAG=mni_adni_nl_1-2
ARGS_VERS=-0.2.1
ARGS_PACKAGE=arguments${ARGS_VERS}
ARGS_GIT=git@github.com:aces/arguments.git
ARGS_GIT_TAG=arguments_0-2-1
ARGS_CVS=libraries/arguments
ARGS_CVS_TAG=arguments_0-2-1
AUTOREG_VERS=-0.99.7
AUTOREG_PACKAGE=mni_autoreg${AUTOREG_VERS}
AUTOREG_GIT=git@github.com:aces/mni_autoreg.git
AUTOREG_GIT_TAG=mni-autoreg_0_99_7
AUTOREG_CVS=registration/mni_autoreg
AUTOREG_CVS_TAG=autoreg-0-99-7
AVG305_VERS=-1.1
AVG305_PACKAGE=mni-models_average305-lin${AVG305_VERS}
AVG305_GIT=git@github.com:aces/mni-models_average305-lin.git
AVG305_GIT_TAG=average305-lin-1-1
AVG305_CVS=mni-models/average305-lin
AVG305_CVS_TAG=average305-lin-1-1
BET_VERS=-1.3.7
BET_PACKAGE=mincbet${BET_VERS}
BET_GIT=git@github.com:aces/mincbet.git
BET_GIT_TAG=bet-1-3-7
BET_CVS=minc_dev/mincbet
BET_CVS_TAG=bet-1-3-7
BICINVENTOR_VERS=-0.3.1
BICINVENTOR_PACKAGE=bicInventor${BICINVENTOR_VERS}
BICINVENTOR_GIT=
BICINVENTOR_GIT_TAG=
BICINVENTOR_CVS=libraries/bicInventor
BICINVENTOR_CVS_TAG=bicinventor_0-3-1
BOOST_VERS=_1_64_0
BOOST_PACKAGE=boost${BOOST_VERS}
BOOST_GIT=
BOOST_GIT_TAG=
BOOST_CVS=
BOOST_CVS_TAG=
BICPL_VERS=-1.4.8
BICPL_PACKAGE=bicpl${BICPL_VERS}
BICPL_GIT=git@github.com:aces/bicpl.git
BICPL_GIT_TAG=bicpl-1_4_8
BICPL_CVS=libraries/bicpl
BICPL_CVS_TAG=bicpl-1_4_8
BRAINVIEW_VERS=-0.8.2
BRAINVIEW_PACKAGE=brain-view${BRAINVIEW_VERS}
BRAINVIEW_GIT=
BRAINVIEW_GIT_TAG=
BRAINVIEW_CVS=visualization/brain-view
BRAINVIEW_CVS_TAG=bv_0_8_2
CAREA_VERS=-1.3.0
CAREA_PACKAGE=cortex_area${CAREA_VERS}
CAREA_GIT=git@github.com:aces/cortex_area.git
CAREA_GIT_TAG=v1-3-0
CAREA_CVS=statistics/cortex_area
CAREA_CVS_TAG=v1-3-0
CGAL_VERS=-3.3.1
CGAL_PACKAGE=CGAL${CGAL_VERS}
CGAL_GIT=
CGAL_GIT_TAG=
CGAL_CVS=
CGAL_CVS_TAG=
CIVET_VERS=-2.1.1
CIVET_PACKAGE=civet${CIVET_VERS}
CIVET_GIT=git@github.com:aces/CIVET.git
CIVET_GIT_TAG=CIVET_2_1_1
CIVET_CVS=pipelines/CIVET
CIVET_CVS_TAG=CIVET_2_1_1
CLASP_VERS=-3.0.3
ifeq ($(CLASP_VERS),-2.1)
CLASP_PACKAGE=CLASP${CLASP_VERS}
else
CLASP_PACKAGE=surface-extraction${CLASP_VERS}
endif
CLASP_GIT=git@github.com:aces/surface-extraction.git
CLASP_GIT_TAG=clasp_3-0-3
CLASP_CVS=surface/surface-extraction
CLASP_CVS_TAG=clasp_3-0-3
CLASSIFY_VERS=-1.1.1
CLASSIFY_PACKAGE=classify${CLASSIFY_VERS}
CLASSIFY_GIT=git@github.com:aces/classify.git
CLASSIFY_GIT_TAG=release-1.1.10
CLASSIFY_CVS=INSECT/classify
CLASSIFY_CVS_TAG=classify-1-1-1
COIN_VERS=-3.1.3
# COIN_VERS=-4.0.0a
COIN_PACKAGE=Coin${COIN_VERS}
COIN_GIT=
COIN_GIT_TAG=
COIN_CVS=
COIN_CVS_TAG=
COLIN27_VERS=-1.2
COLIN27_PACKAGE=mni-models_colin27-lin${COLIN27_VERS}
COLIN27_GIT=git@github.com:aces/mni-models_colin27-lin.git
COLIN27_GIT_TAG=colin27-lin-1-2
COLIN27_CVS=mni-models/colin27-lin
COLIN27_CVS_TAG=colin27-lin-1-2
CONGLOMERATE_VERS=-1.6.9
CONGLOMERATE_PACKAGE=conglomerate${CONGLOMERATE_VERS}
CONGLOMERATE_GIT=git@github.com:aces/conglomerate.git
CONGLOMERATE_GIT_TAG=conglomerate_1-6-9
CONGLOMERATE_CVS=libraries/conglomerate
CONGLOMERATE_CVS_TAG=conglomerate_1-6-9
CSURFACE_VERS=-1.2.2
CSURFACE_PACKAGE=cortical_surface${CSURFACE_VERS}
CSURFACE_GIT=git@github.com:aces/cortical_surface.git
CSURFACE_GIT_TAG=cortical-surface-1-2-2
CSURFACE_CVS=surface/cortical_surface
CSURFACE_CVS_TAG=cortical-surface-1-2-2
DISPLAY_VERS=-1.6.0
DISPLAY_PACKAGE=Display${DISPLAY_VERS}
DISPLAY_GIT=
DISPLAY_GIT_TAG=
DISPLAY_CVS=
DISPLAY_CVS_TAG=
EBTKS_VERS=-1.6.6
ifeq ($(EBTKS_VERS),-1.4)
EBTKS_PACKAGE=EBTKS${EBTKS_VERS}
else
EBTKS_PACKAGE=ebtks${EBTKS_VERS}
endif
EBTKS_GIT=git@github.com:aces/EBTKS.git
EBTKS_GIT_TAG=ebtks-1_6_6
EBTKS_CVS=libraries/EBTKS
EBTKS_CVS_TAG=ebtks-1-6-6
EMMA_VERS=-1.0.0
EMMA_PACKAGE=emma${EMMA_VERS}
EMMA_GIT=
EMMA_GIT_TAG=
EMMA_CVS=
EMMA_CVS_TAG=
GETOPT_VERS=-0.3
GETOPT_PACKAGE=Getopt-Tabular${GETOPT_VERS}
GETOPT_GIT=git@github.com:aces/Getopt-Tabular.git
GETOPT_GIT_TAG=getopt_0-3
GETOPT_CVS=libraries/Getopt-Tabular
GETOPT_CVS_TAG=getopt_0-3
GGS_VERS=-9.22
GGS_PACKAGE=ghostscript${GGS_VERS}
GGS_GIT=
GGS_GIT_TAG=
GGS_CVS=
GGS_CVS_TAG=
GLIM_VERS=-1.2
GLIM_PACKAGE=glim_image${GLIM_VERS}
GLIM_GIT=
GLIM_GIT_TAG=
GLIM_CVS=
GLIM_CVS_TAG=
GSL_VERS=-1.8
GSL_PACKAGE=gsl${GSL_VERS}
GSL_GIT=
GSL_GIT_TAG=
GSL_CVS=
GSL_CVS_TAG=
HDF_VERS=5-1.8.8
HDF_PACKAGE=hdf${HDF_VERS}
HDF_GIT=
HDF_GIT_TAG=
HDF_CVS=
HDF_CVS_TAG=
ICBM152_VERS=-1.1
ICBM152_PACKAGE=mni-models_icbm152-lin${ICBM152_VERS}
ICBM152_GIT=git@github.com:aces/mni-models_icbm152-lin.git
ICBM152_GIT_TAG=mni_icbm_lin_1-1
ICBM152_CVS=mni-models/icbm152-lin
ICBM152_CVS_TAG=release_1-1
ICBM152NL_VERS=-1.1
ICBM152NL_PACKAGE=mni-models_icbm152-nl${ICBM152NL_VERS}
ICBM152NL_GIT=git@github.com:aces/mni-models_icbm152-nl.git
ICBM152NL_GIT_TAG=mni_icbm_nl_1-1
ICBM152NL_CVS=mni-models/icbm152-nl
ICBM152NL_CVS_TAG=mni_icbm_nl_1-1
ICBM152NL09_VERS=-1.1
ICBM152NL09_PACKAGE=mni-models_icbm152-nl-2009${ICBM152NL09_VERS}
ICBM152NL09_GIT=git@github.com:aces/mni-models_icbm152-nl-2009.git
ICBM152NL09_GIT_TAG=mni_icbm_nl_09a_1-1
ICBM152NL09_CVS=mni-models/icbm152-nl-2009
ICBM152NL09_CVS_TAG=mni_icbm_nl_09a_1-1
ICBMTEMP_VERS=-1.0
ICBMTEMP_PACKAGE=mni-templates${ICBMTEMP_VERS}
ICBMTEMP_GIT=git@github.com:aces/mni-templates.git
ICBMTEMP_GIT_TAG=mni_templates_1-0
ICBMTEMP_CVS=mni-models/mni-templates
ICBMTEMP_CVS_TAG=mni_templates_1-0
ILT_VERS=-1.2.5
ILT_PACKAGE=ILT${ILT_VERS}
ILT_GIT=git@github.com:aces/ILT.git
ILT_GIT_TAG=ILT-1_2_5
ILT_CVS=libraries/ILT
ILT_CVS_TAG=ILT-1_2_5
IMAGEMAGICK_VERS=-7.0.1-8
IMAGEMAGICK_PACKAGE=ImageMagick${IMAGEMAGICK_VERS}
IMAGEMAGICK_GIT=
IMAGEMAGICK_GIT_TAG=
IMAGEMAGICK_CVS=
IMAGEMAGICK_CVS_TAG=
INORM_VERS=-1.0.4
INORM_PACKAGE=inormalize${INORM_VERS}
INORM_GIT=git@github.com:aces/inormalize.git
INORM_GIT_TAG=inormalize_1-0-4
INORM_CVS=INSECT/inormalize
INORM_CVS_TAG=inormalize_1-0-4
LOBESEG_VERS=-1.1
LOBESEG_PACKAGE=mni_lobe_segment${LOBESEG_VERS}
LOBESEG_GIT=
LOBESEG_GIT_TAG=
LOBESEG_CVS=INSECT/mni_lobe_segment
LOBESEG_CVS_TAG=lobe_segment_1-1
LAPLACE_VERS=-1.3.0
LAPLACE_PACKAGE=laplacian_thickness${LAPLACE_VERS}
LAPLACE_GIT=git@github.com:aces/laplacian_thickness.git
LAPLACE_GIT_TAG=laplace-1-3-0
LAPLACE_CVS=surface/laplacian_thickness/
LAPLACE_CVS_TAG=laplace-1-3-0
M4_VERS=-1.0
M4_PACKAGE=m4
M4_GIT=git@github.com:aces/m4.git
M4_GIT_TAG=civet-2.1.0
M4_CVS=libraries/mni-acmacros
M4_CVS_TAG=m4_1-0
MINC_VERS=-2.1.02
MINC_PACKAGE=minc${MINC_VERS}
MINC_GIT=git@github.com:aces/minc.git
MINC_GIT_TAG=minc-2-1-02
MINC_CVS=libraries/minc
MINC_CVS_TAG=minc2-1-02
MRISIM_VERS=-1.0.3
MRISIM_PACKAGE=mrisim${MRISIM_VERS}
MRISIM_GIT=
MRISIM_GIT_TAG=
MRISIM_CVS=simulation/mrisim
MRISIM_CVS_TAG=mrisim-1-0-3
N3_VERS=-1.12.3
N3_PACKAGE=N3${N3_VERS}
N3_GIT=git@github.com:aces/N3.git
N3_GIT_TAG=N3-1_12_3
N3_CVS=INSECT/N3
N3_CVS_TAG=N3-1_12_3
NETCDF_VERS=-3.6.1
NETCDF_PACKAGE=netcdf${NETCDF_VERS}
NETCDF_GIT=
NETCDF_GIT_TAG=
NETCDF_CVS=
NETCDF_CVS_TAG=
NETPBM_VERS=-10.35.94
NETPBM_PACKAGE=netpbm${NETPBM_VERS}
NETPBM_GIT=
NETPBM_GIT_TAG=
NETPBM_CVS=
NETPBM_CVS_TAG=
OOBICPL_VERS=-0.4.9
OOBICPL_PACKAGE=oobicpl${OOBICPL_VERS}
OOBICPL_GIT=git@github.com:aces/oobicpl.git
OOBICPL_GIT_TAG=oobicpl-0-4-9
OOBICPL_CVS=libraries/oobicpl
OOBICPL_CVS_TAG=oobicpl-0-4-9
PCREPP_VERS=-0.9.5
PCREPP_PACKAGE=pcre++${PCREPP_VERS}
PCREPP_GIT=
PCREPP_GIT_TAG=
PCREPP_CVS=
PCREPP_CVS_TAG=
PCRE_VERS=-7.8
PCRE_PACKAGE=pcre${PCRE_VERS}
PCRE_GIT=
PCRE_GIT_TAG=
PCRE_CVS=
PCRE_CVS_TAG=
PERLLIB_VERS=-0.09
PERLLIB_PACKAGE=mni_perllib${PERLLIB_VERS}
PERLLIB_GIT=git@github.com:aces/mni-perllib.git
PERLLIB_GIT_TAG=mni_perllib_v0_09
PERLLIB_CVS=libraries/mni-perllib
PERLLIB_CVS_TAG=mni_perllib_v0_09
PMP_VERS=-0.8.3
PMP_PACKAGE=PMP${PMP_VERS}
PMP_GIT=git@github.com:aces/PMP.git
PMP_GIT_TAG=ver-0-8-3
PMP_CVS=libraries/PMP
PMP_CVS_TAG=ver-0-8-3
PVE_VERS=-1.4.3
PVE_PACKAGE=pve${PVE_VERS}
PVE_GIT=git@github.com:aces/pve.git
PVE_GIT_TAG=ver-1_4_3
PVE_CVS=INSECT/pve
PVE_CVS_TAG=ver-1_4_3
QVAL_VERS=_1.38.0
QVAL_PACKAGE=qvalue${QVAL_VERS}
QVAL_GIT=
QVAL_GIT_TAG=
QVAL_CVS=
QVAL_CVS_TAG=
RAY_TRACE_VERS=-1.0.4
RAY_TRACE_PACKAGE=ray_trace${RAY_TRACE_VERS}
RAY_TRACE_GIT=git@github.com:aces/ray_trace.git
RAY_TRACE_GIT_TAG=ray-trace-1-0-4
RAY_TRACE_CVS=visualization/ray_trace
RAY_TRACE_CVS_TAG=ray-trace-1-0-4
REGISTER_VERS=-1.4.0
REGISTER_PACKAGE=Register${REGISTER_VERS}
REGISTER_GIT=
REGISTER_GIT_TAG=
REGISTER_CVS=
REGISTER_CVS_TAG=
RMINC_VERS=_0.5.1
RMINC_PACKAGE=RMINC${RMINC_VERS}
RMINC_GIT=
RMINC_GIT_TAG=
RMINC_CVS=
RMINC_CVS_TAG=
RSTAT_VERS=-0.9.4
RSTAT_PACKAGE=mni_cortical_statistics${RSTAT_VERS}
RSTAT_GIT=
RSTAT_GIT_TAG=
RSTAT_CVS=
RSTAT_CVS_TAG=
SIMAGE_VERS=-1.7.0
SIMAGE_PACKAGE=simage${SIMAGE_VERS}
SIMAGE_GIT=
SIMAGE_GIT_TAG=
SIMAGE_CVS=
SIMAGE_CVS_TAG=
# SOQT_VERS=-1.4.2a
SOQT_VERS=-1.5.0
SOQT_PACKAGE=SoQt${SOQT_VERS}
SOQT_GIT=
SOQT_GIT_TAG=
SOQT_CVS=
SOQT_CVS_TAG=
STXSEG_VERS=-1.0
STXSEG_PACKAGE=mni_stx_segment${STXSEG_VERS}
STXSEG_GIT=
STXSEG_GIT_TAG=
STXSEG_CVS=INSECT/mni_stx_segment
STXSEG_CVS_TAG=stx_segment_1-0
SURFREG_VERS=-0.6.4
ifeq ($(SURFREG_VERS),-0.4)
SURFREG_PACKAGE=mni-surfreg${SURFREG_VERS}
else
SURFREG_PACKAGE=mni_surfreg${SURFREG_VERS}
endif
SURFREG_GIT=git@github.com:aces/mni_surfreg.git
SURFREG_GIT_TAG=mni-surfreg-0-6-4
SURFREG_CVS=registration/mni_surfreg
SURFREG_CVS_TAG=mni-surfreg-0-6-4
TRUEFONT_VERS=-2.0
TRUEFONT_PACKAGE=urw-fonts${TRUEFONT_VERS}
TRUEFONT_GIT=
TRUEFONT_GIT_TAG=
TRUEFONT_CVS=
TRUEFONT_CVS_TAG=
# +---------------------+
# | NAMES OF PACKAGES |
# +---------------------+
TGZ_FLAG=${PWD}/TGZ/.tgz_created
TGZ_DIR=${PWD}/TGZ
# +---------------+
# | BOOST STUFF |
# +---------------+
ifeq ($(BOOST_VERS),_1_48_0)
BJAM := ${SOURCE_DIR}/${BOOST_PACKAGE}/tools/build/v2/engine/${JAMARCH}
endif
ifeq ($(BOOST_VERS),_1_64_0)
BJAM := ${SOURCE_DIR}/${BOOST_PACKAGE}
endif
BOOSTTMP := /tmp
# +--------------------------------------------------+
# | DEFINE THE VARIABLES FOR THE NAME OF PACKAGES. |
# | MOST PACKAGES ARE .tar.gz, EXCEPT A FEW |
# | EXCEPTIONS. |
# +--------------------------------------------------+
LIST_EXTRA = BICINVENTOR BRAINVIEW COIN DISPLAY EMMA GLIM \
QVAL REGISTER RMINC RSTAT SIMAGE SOQT TRUEFONT
LIST_TAR = ADNI ARGS AUTOREG AVG305 BET BOOST BICPL CAREA NETCDF \
CGAL CIVET CLASP CLASSIFY COLIN27 CONGLOMERATE CSURFACE EBTKS \
GETOPT GSL HDF ICBM152 ICBM152NL ICBM152NL09 ICBMTEMP ILT \
INORM LAPLACE M4 MINC N3 OOBICPL PCREPP PCRE PERLLIB PMP PVE \
RAY_TRACE SURFREG
ifeq ($(MAGICK),yes)
LIST_TAR += IMAGEMAGICK
endif
ifeq ($(ANIMAL),yes)
LIST_TAR += LOBESEG STXSEG
endif
ifeq ($(MRI_SIM),yes)
LIST_TAR += MRISIM
endif
LIST_TGZ = NETPBM
ifeq ($(GGS_VERS),-8.71.1)
LIST_BZ2 = GGS
endif
ifeq ($(GGS_VERS),-9.22)
LIST_BZ2 =
LIST_TAR += GGS
endif
define make-variables
$1_TAR = ${TGZ_DIR}/${$1_PACKAGE}.$2
$1_DIR = ${SOURCE_DIR}/${$1_PACKAGE}
$1_UNTAR = ${SOURCE_DIR}/${$1_PACKAGE}/.$1_created
endef
$(foreach element,$(LIST_TAR),$(eval $(call make-variables,$(element),tar.gz)))
$(foreach element,$(LIST_TGZ),$(eval $(call make-variables,$(element),tgz)))
$(foreach element,$(LIST_BZ2),$(eval $(call make-variables,$(element),tar.bz2)))
# Special case to redefine M4 without version tag.
M4_DIR = ${SOURCE_DIR}/m4
####################################################################################
# +---------------+
# | MAKE TGZ DIR |
# +---------------+
${TGZ_FLAG}:
mkdir -p ${TGZ_DIR}
@if [ ! -f $@ ] ; then \
echo 1 > $@ ; \
fi
# +-----------------------+
# | MAKE QUARANTINE DIRS |
# +-----------------------+
$(QUARANTINE_FLAG):
mkdir -p ${SOURCE_DIR}
mkdir -p $(PREFIX_PATH)/lib $(PREFIX_PATH)/include $(PREFIX_PATH)/man/man1 $(PREFIX_PATH)/man/man2 $(PREFIX_PATH)/man/man3 $(PREFIX_PATH)/man/man4 $(PREFIX_PATH)/man/man5 $(PREFIX_PATH)/man/man6 $(PREFIX_PATH)/man/man7 $(PREFIX_PATH)/man/man8 $(PREFIX_PATH)/man/man9 $(PREFIX_PATH)/perl
@if [ ! -f $@ ] ; then \
echo 1 > $@ ; \
fi
@echo "# +-------------------------------------------------+"
@echo "# | SRC = ${SOURCE_PATH}"
@echo "# | PREFIX = ${PREFIX_PATH}"
@echo "# | CFLAGS = $(CFLAGS)"
@echo "# | CPPFLAGS = $(CPPFLAGS)"
@echo "# | CXXFLAGS = $(CXXFLAGS)"
@echo "# | LDFLAGS = $(LDFLAGS)"
@echo "# +-------------------------------------------------+"
# +-----------------------+
# | OBTAIN THE SOURCES: |
# | - FROM PACKAGE |
# | - FROM GIT |
# | - FROM CVS |
# +-----------------------+
define make-untar-target
$($1_UNTAR): ${QUARANTINE_FLAG}
@if [ ! -d ${$1_DIR} ] ; then \
if [ -e ${$1_TAR} ] ; then \
if [[ "${$1_TAR}" =~ "tgz" ]] || [[ "${$1_TAR}" =~ "tar.gz" ]] ; then \
${GTAR} -zxf ${$1_TAR} --directory=${SOURCE_DIR} ; \
else \
if [[ "${$1_TAR}" =~ "bz2" ]] ; then \
${GTAR} -xjf ${$1_TAR} --directory=${SOURCE_DIR} ; \
fi ; \
fi ; \
else \
if [ "$(USE_CVS)" == "yes" ] ; then \
cvs co -P -r ${$1_CVS_TAG} -d ${$1_DIR} ${$1_CVS} ; \
else \
if [ "$(USE_GIT)" == "yes" ] ; then \
if [ -n "${$1_GIT}" ] ; then \
git lfs clone --recurse-submodules --branch ${$1_GIT_TAG} ${$1_GIT} ${$1_DIR}; \
if [ ! -e ${$1_DIR}/.git ] ; then \
echo "Fail to clone source codes from ${$1_GIT}"; \
exit 1; \
fi ; \
cd ${$1_DIR}; \
if [[ "`git describe --tags`" != "${$1_GIT_TAG}" ]] ; then \
echo "Fail to checkout tag to ${$1_GIT_TAG}"; \
exit 1; \
fi ; \
cd -; \
else \
echo "Warning: no git repo for $1" ; \
fi ; \
else \
echo "You need either USE_GIT=yes or USE_CVS=yes" ; \
exit 1; \
fi ; \
fi ; \
fi ; \
if [ -d ${$1_DIR} ] ; then \
touch ${$1_UNTAR} ; \
fi ; \
fi
endef
LIST_ALL = ${LIST_TAR} ${LIST_TGZ} ${LIST_BZ2}
$(foreach element,$(LIST_ALL),$(eval $(call make-untar-target,$(element))))
# +------------------------------------+
# | MAIN LIBRARIES AND CORE PROGRAMS |
# +------------------------------------+
ADNI = $(PREFIX_PATH)/share/mni-models/mni_adni_t1w_tal_nlin_asym.mnc
LIBARGS = $(PREFIX_PATH)/lib/libarguments.a
AVG305VBM = $(PREFIX_PATH)/share/avg305/average_305_mask_1mm.mnc
AUTOREG = $(PREFIX_PATH)/bin/make_model
AVG305 = $(PREFIX_PATH)/share/mni-models/average305_t1_tal_lin.mnc
BRAINVIEW = $(PREFIX_PATH)/bin/brain-view
CAREA = $(PREFIX_PATH)/bin/cortex_area
CIVET = $(PREFIX_PATH)/CIVET$(CIVET_VERS)/CIVET_Processing_Pipeline
CLASP = $(PREFIX_PATH)/bin/expand_from_white
CLASSIFY = $(PREFIX_PATH)/bin/classify
LIBCOIN = $(PREFIX_PATH)/lib/libCoin.$(LIB_EXT)
COLIN27 = $(PREFIX_PATH)/share/mni-models/colin27_t1_tal_lin.mnc
CONGLOMERATE = $(PREFIX_PATH)/bin/volume_object_evaluate
CORTICAL = $(PREFIX_PATH)/bin/deform_surface
MNIDISPLAY = $(PREFIX_PATH)/bin/Display
GGS = $(PREFIX_PATH)/bin/gs
GLIM = $(PREFIX_PATH)/bin/glim_image
ICBM152 = $(PREFIX_PATH)/share/mni-models/icbm_avg_152_pd_tal_lin.mnc
ICBM152NL = $(PREFIX_PATH)/share/mni-models/icbm_avg_152_t1_tal_nlin_symmetric_VI.mnc
ICBM152NL09 = $(PREFIX_PATH)/share/mni-models/mni_icbm152_pd_tal_nlin_asym_09a.mnc
ICBMTEMP = $(PREFIX_PATH)/share/ICBM/icbm_template_1.00mm.mnc
IMAGEMAGICK = $(PREFIX_PATH)/bin/convert
INORM = $(PREFIX_PATH)/bin/headmask
LAPLACE = $(PREFIX_PATH)/bin/laplacian_thickness $(PREFIX_PATH)/bin/normal_thickness
LIBBICINVENTOR = $(PREFIX_PATH)/lib/libbicInventor.a
LIBBICPL = $(PREFIX_PATH)/lib/libbicpl.$(LIB_EXT)
LIBEBTKS = $(PREFIX_PATH)/lib/libEBTKS.a
EMMA = $(PREFIX_PATH)/emma/mireadvar.$(MEX_EXT) $(PREFIX_PATH)/bin/micreateimage
LIBGSL = $(PREFIX_PATH)/lib/libgsl.a
LIBHDF = $(PREFIX_PATH)/lib/libhdf5.a