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.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