submission

3 files changed, 175 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..15d97d3b6a92
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,33 @@
+pkgbase = minc-toolkit-v2
+	pkgdesc = Medical Imaging NetCDF Toolkit
+	pkgver = 1.9.15
+	pkgrel = 1
+	url = https://www.mcgill.ca/bic/software/minc
+	arch = any
+	license = GPL3
+	makedepends = git
+	makedepends = cmake
+	makedepends = bc
+	makedepends = libhdf5
+	depends = perl
+	depends = libjpeg-turbo
+	depends = libxi
+	depends = libxmu
+	depends = libgl
+	depends = glu
+	depends = fftw
+	depends = glut
+	depends = netcdf
+	depends = pcre
+	depends = zlib
+	depends = hdf5
+	depends = nifticlib
+	depends = insight-toolkit
+	provides = minc-toolkit
+	source = git+https://github.com/BIC-MNI/minc-toolkit-v2.git
+	source = FindNIFTI.patch
+	sha512sums = SKIP
+	sha512sums = 28e12be5c8c7e397a063fa570fd4819dc45daf845a608164b9e7aec6fb6fb99d58f4f494d648147613bb80393b88d40f63748ea9f6096d96a1df1e66d17bbed7
+
+pkgname = minc-toolkit-v2
+
diff --git a/FindNIFTI.patch b/FindNIFTI.patch
new file mode 100644
index 000000000000..f473790a4d98
--- /dev/null
+++ b/FindNIFTI.patch
@@ -0,0 +1,16 @@
+--- cmake-modules/FindNIFTI.cmake.bak	2017-10-28 08:50:48.314047843 +0200
++++ cmake-modules/FindNIFTI.cmake	2017-10-28 08:51:53.744047118 +0200
+@@ -1,11 +1,11 @@
+ # FindNIFTI.cmake module
+ 
+ 
+-FIND_PATH(NIFTI_INCLUDE_DIR nifti1_io.h /usr/include /usr/local/include /usr/local/bic/include)
++FIND_PATH(NIFTI_INCLUDE_DIR nifti1_io.h /usr/include/nifti /usr/include /usr/local/include /usr/local/bic/include)
+ 
+ FIND_LIBRARY(NIFTI_LIBRARY NAMES niftiio PATHS /usr/lib /usr/local/lib /usr/local/bic/lib)
+ 
+-FIND_PATH(ZNZ_INCLUDE_DIR znzlib.h /usr/include /usr/local/include /usr/local/bic/include)
++FIND_PATH(ZNZ_INCLUDE_DIR znzlib.h /usr/include/nifti /usr/include /usr/local/include /usr/local/bic/include)
+ 
+ FIND_LIBRARY(ZNZ_LIBRARY NAMES znz PATHS /usr/lib /usr/local/lib /usr/local/bic/lib)
+ 
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..178f0d45a990
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,126 @@
+# PKBGUILD: Martino Pilia <martino.pilia@gmail.com>
+pkgname=minc-toolkit-v2
+pkgver=1.9.15
+pkgrel=1
+pkgdesc="Medical Imaging NetCDF Toolkit"
+arch=('any')
+url="https://www.mcgill.ca/bic/software/minc"
+license=('GPL3')
+depends=('perl' 'libjpeg-turbo' 'libxi' 'libxmu' 'libgl' 'glu' 'fftw' 'glut' 'netcdf' 'pcre' 'zlib' 'hdf5' 'nifticlib' 'insight-toolkit')
+makedepends=('git' 'cmake' 'bc' 'libhdf5')
+provides=('minc-toolkit')
+source=('git+https://github.com/BIC-MNI/minc-toolkit-v2.git'
+		'FindNIFTI.patch')
+sha512sums=('SKIP'
+            '28e12be5c8c7e397a063fa570fd4819dc45daf845a608164b9e7aec6fb6fb99d58f4f494d648147613bb80393b88d40f63748ea9f6096d96a1df1e66d17bbed7')
+
+_release_commit="29273c3f065c86496c6a1270355077b534e676a3"
+
+_itk=`ls /usr/lib/cmake | grep -m1 ITK`
+_install_prefix="/usr/share/minc"
+
+prepare() {
+
+	# ensure that the required ITK modules are present
+	if [ `ls "/usr/include/$_itk" | grep 'itkMINCImageIO.h'` == "" ];
+	then
+		echo "ERROR: ITK must be built with -DModule_ITKIOMINC:BOOL=ON"
+		exit 1
+	fi
+	if [ `ls "/usr/include/$_itk" | grep 'itkMINCTransformAdapter.h'` == "" ];
+	then
+		echo "ERROR: ITK must be built with -DModule_ITKIOTransformMINC:BOOL=ON"
+		exit 1
+	fi
+
+	cd "$srcdir/$pkgname"
+	git checkout $_release_commit
+	git submodule update --init --recursive
+
+	# that hash seems to be wrong
+	sed -i \
+		's/5c9dad3705a3408d27f696e5b31fb88c/41fe6758d46cccb1675693d155ee7001/' \
+		cmake-modules/BuildNETCDF.cmake
+
+	# find system NIFTI in the right place
+	sed -i \
+		's/FIND_PACKAGE(NIFTI OPTIONAL)/FIND_PACKAGE(NIFTI REQUIRED)/' \
+		CMakeLists.txt
+	patch -p0 -i ${srcdir}/FindNIFTI.patch
+
+	# static version of HDF5
+	sed -i \
+		'74iSET(HDF5_LIBRARY "/usr/lib/libhdf5.a")' \
+		cmake-modules/FindHDF5.cmake
+	sed -i \
+		'75iSET(HDF5_LIBRARIES ${HDF5_LIBRARY})' \
+		cmake-modules/FindHDF5.cmake
+
+	# libminc for patch_morphology
+	sed -i \
+		'5iINCLUDE_DIRECTORIES(${LIBMINC_INCLUDE_DIRS})' \
+		patch_morphology/legacy/CMakeLists.txt
+	sed -i \
+		'6iLINK_DIRECTORIES(${LIBMINC_LIBRARY_DIRS})' \
+		patch_morphology/legacy/CMakeLists.txt
+
+	# the compiler won't like this
+	sed -i \
+		's/enum {false=0, true=1};//' \
+		minctools/progs/mincdump/mincdump.h
+
+    mkdir build || :
+    cd build
+
+    cmake .. \
+        -DCMAKE_BUILD_TYPE:STRING=Release   \
+        -DCMAKE_INSTALL_PREFIX:PATH="${pkgdir}${_install_prefix}" \
+        -DMT_BUILD_ABC:BOOL=ON   \
+        -DMT_BUILD_ANTS:BOOL=ON   \
+        -DMT_BUILD_C3D:BOOL=ON   \
+        -DMT_BUILD_ELASTIX:BOOL=ON   \
+        -DMT_BUILD_IM:BOOL=OFF   \
+        -DMT_BUILD_ITK_TOOLS:BOOL=ON   \
+        -DMT_BUILD_LITE:BOOL=OFF   \
+        -DMT_BUILD_SHARED_LIBS:BOOL=ON   \
+        -DMT_BUILD_VISUAL_TOOLS:BOOL=ON   \
+        -DMT_USE_OPENMP:BOOL=ON   \
+        -DUSE_SYSTEM_FFTW3D:BOOL=ON   \
+        -DUSE_SYSTEM_FFTW3F:BOOL=ON   \
+        -DUSE_SYSTEM_GLUT:BOOL=ON   \
+        -DUSE_SYSTEM_GSL:BOOL=ON   \
+        -DUSE_SYSTEM_HDF5:BOOL=ON   \
+        -DUSE_SYSTEM_ITK:BOOL=ON   \
+        -DUSE_SYSTEM_NETCDF:BOOL=ON   \
+        -DUSE_SYSTEM_NIFTI:BOOL=ON   \
+        -DUSE_SYSTEM_PCRE:BOOL=ON   \
+        -DUSE_SYSTEM_ZLIB:BOOL=ON \
+		-DITK_DIR:PATH=/usr/lib/cmake/$_itk
+}
+
+build() {
+    cd "$srcdir/$pkgname/build"
+    make
+}
+
+#check() {
+#	cd "$srcdir/$pkgname/build"
+#	make test
+#}
+
+package() {
+	cd "$srcdir/$pkgname/build"
+
+	make install
+
+	cd "${pkgdir}${_install_prefix}"
+	rm -rf minc-toolkit-config*
+
+	mkdir -p $pkgdir/usr/share/bash-completion/completions
+	mv share/bashcomp.sh $pkgdir/usr/share/bash-completion/completions/c3d
+	mv bin $pkgdir/usr/bin
+	mv include $pkgdir/usr/include
+	mv lib $pkgdir/usr/lib
+	mv man $pkgdir/usr/share/man
+}
+