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module purge module load misc/bison/3.0 module load misc/flex/2.6.4 module load library/zlib/1.2.11 module load NetCDF/4.4.1.1-gnu module load library/hdf5/1.8.18-parallel module load pcre/10.23 module load gsl/2.3 module load fftw/3.2.2-gnu module load cmake/3.8.2 module load misc/curl/7.54.0 module load misc/openssl/1.0.2 module load misc/libarchive/3.3.1 module load library/expat/2.2.0 module load misc/libssh2/1.8.0 module load misc/nifticlib/2.0.0 cd /sw/imagingsw/minc-toolkit/src/minc-toolkit-v2-1.9.11 >>>>>>>>>>>>>>>>> The following had to be done as some of the packages have been hard coded and they are no longer available ********************* vi cmake-modules/BuildZLIB.cmake URL "http://zlib.net/zlib-1.2.11.tar.gz" URL_MD5 "1c9f62f0778697a09d36121ead88e08e" ********************** #change everywhere you see https to http vi cmake-modules/BuildHDF5.cmake ExternalProject_Add(HDF5 URL "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.15-patch1/src/hdf5-1.8.15-patch1.tar.bz2" *********************** cmake-modules/BuildNIFTI.cmake https://nchc.dl.sourceforge.net/project/niftilib/nifticlib/nifticlib_2_0_0/nifticlib-2.0.0.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> vi CMakeLists.txt change from OFF to ON for ZLIB # superbuild options OPTION(MT_BUILD_LITE "Build lite version of minc-toolkit, without ITK or visual tools" OFF) OPTION(MT_BUILD_SHARED_LIBS "Build shared libraries." ON) OPTION(USE_SYSTEM_ZLIB "Use System ZLIB " ON) #OPTION(USE_SYSTEM_NIFTI "Use System NIFTI " OFF) #OPTION(USE_SYSTEM_GIFTI "Use System GIfTI" OFF) OPTION(USE_SYSTEM_NETCDF "Use System NETCDF > 3.6.3" ON) OPTION(USE_SYSTEM_HDF5 "Use System HDF5 > 1.8" ON) OPTION(USE_SYSTEM_PCRE "Use System PCRE " ON) OPTION(USE_SYSTEM_GSL "Use System GSL " ON) OPTION(USE_SYSTEM_FFTW3F "Use System FFTW3F " OFF) OPTION(USE_SYSTEM_FFTW3D "Use System FFTW3D " OFF) OPTION(USE_SYSTEM_GLUT "Use System GLUT " ON) OPTION(MT_BUILD_ITK_TOOLS "Build ITK-based tools" OFF) OPTION(MT_BUILD_VISUAL_TOOLS "Build visual tools (Display, Register, postf, ray_trace) requires OpenGL & Glut" OFF) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> cd /sw/imagingsw/minc-toolkit/src/minc-toolkit-v2-1.9.11 rm -r -f build;mkdir build;cd build;cmake -DCMAKE_INSTALL_PREFIX=/sw/imagingsw/minc-toolkit/2-1.9.11 -DZLIB_LIBRARIES=/sw/library/zlib/1.2.11/lib .. 2>&1 | tee cmakeLog.tx;txt make 2>&1 | tee makeLog.txt #mkdir build && cd build #cmake -DCMAKE_INSTALL_PREFIX=/sw/imagingsw/minc-toolkit/2-1.9.11 -DZLIB_LIBRARIES=/sw/library/zlib/1.2.11/lib .. 2>&1 | tee cmakeLog.txt # Enter the location of all dependencies, if not detected automatically make 2>&1 | tee makelog.txt make test 2>&1 | tee makeTestlog.txt make install 2>&1 | tee makeInstalllog.txt >>>>>>> ###Following packages are needed to compile all tools: * Perl - http://www.perl.org/ ***** BISON - http://www.gnu.org/software/bison/ ***** FLEX - http://flex.sf.net/ ***** GLUT - http://freeglut.sourceforge.net/ ***** libxi ***** libxmu ###Following packages are optional (i.e thay can be build as part of superbuild) * zlib - http://zlib.net/ http://zlib.net/zlib-1.2.6.tar.gz * NETCDF - http://www.unidata.ucar.edu/software/netcdf/ ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.0.1.tar.gz * HDF5 - http://www.hdfgroup.org/HDF5/ http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.8/src/hdf5-1.8.8.tar.gz * PCRE - http://www.pcre.org/ http://downloads.sourceforge.net/project/pcre/pcre/8.12/pcre-8.12.tar.gz * GSL - http://www.gnu.org/software/gsl/ ftp://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz * FFTW3 - http://www.fftw.org/ http://www.fftw.org/fftw-3.3.2.tar.gz |
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