gnu: Add itk-snap.
* gnu/packages/image-processing.scm (itk-snap): New variable.
This commit is contained in:
Ricardo Wurmus
Ricardo Wurmus
parent
07f36b0c53
commit
1c4e6aa938
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@ -38,6 +38,7 @@
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#:use-module (gnu packages boost)
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#:use-module (gnu packages check)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages curl)
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#:use-module (gnu packages documentation)
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#:use-module (gnu packages flex)
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#:use-module (gnu packages fontutils)
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@ -60,6 +61,7 @@
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#:use-module (gnu packages protobuf)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages qt)
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#:use-module (gnu packages serialization)
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#:use-module (gnu packages tbb)
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#:use-module (gnu packages tls)
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@ -702,3 +704,140 @@ combine the information contained in both.")
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"InsightToolkit-" version ".tar.xz"))
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(sha256
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(base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))))
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(define-public itk-snap
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(package
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(name "itk-snap")
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(version "3.8.0")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://git.code.sf.net/p/itk-snap/src")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))))
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(build-system cmake-build-system)
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(arguments
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`(#:configure-flags
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(list "-DSNAP_VERSION_GIT_SHA1=release"
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"-DSNAP_VERSION_GIT_BRANCH=release"
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"-DSNAP_VERSION_GIT_TIMESTAMP=0"
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"-DSNAP_PACKAGE_QT_PLUGINS=OFF"
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"-DCMAKE_POSITION_INDEPENDENT_CODE=ON"
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"-DCMAKE_CXX_FLAGS=-std=gnu++11 -fpermissive")
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#:phases
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(modify-phases %standard-phases
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;; During the installation phase all libraries provided by all
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;; dependencies will be copied to the lib directory. That's insane,
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;; so we disable this.
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(add-after 'unpack 'do-not-copy-dependencies
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(lambda _
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(substitute* "CMakeLists.txt"
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(("install_qt5_executable\
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\\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)")
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""))
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#t))
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(add-after 'unpack 'disable-gui-tests
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(lambda _
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;; The GUI tests just time out.
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(substitute* "CMakeLists.txt"
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((" (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
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|RandomForest|RandomForestBailOut)")
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""))
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#t))
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(add-after 'unpack 'make-reproducible
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(lambda _
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(substitute* "CMakeLists.txt"
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(("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
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"SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))
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#t))
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(add-after 'unpack 'prepare-submodules
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(lambda* (#:key inputs #:allow-other-keys)
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(rmdir "Submodules/c3d")
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(copy-recursively (assoc-ref inputs "c3d-src")
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"Submodules/c3d")
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(substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx"
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"Submodules/c3d/adapters/ApplyMetric.cxx")
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(("vcl_") "std::"))
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(rmdir "Submodules/greedy")
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(symlink (assoc-ref inputs "greedy-src")
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"Submodules/greedy")
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#t))
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(add-after 'unpack 'fix-includes
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(lambda _
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(substitute* "GUI/Model/RegistrationModel.cxx"
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(("<vnl_symmetric_eigensystem.h>")
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"<vnl/algo/vnl_symmetric_eigensystem.h>"))
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#t))
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(add-before 'check 'prepare-tests
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(lambda _
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;; Needed by at least one test.
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(setenv "HOME" "/tmp")
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#t))
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(add-after 'install 'wrap-executable
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out")))
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(wrap-program (string-append out "/bin/itksnap")
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`("QT_PLUGIN_PATH" ":" prefix
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,(map (lambda (label)
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(string-append (assoc-ref inputs label)
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"/lib/qt5/plugins"))
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'("qtbase" "qtdeclarative"))))
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#t))))))
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(inputs
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`(("curl" ,curl)
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("fftw" ,fftw)
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("fftwf" ,fftwf)
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("glu" ,glu)
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("hdf5" ,hdf5)
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("mesa" ,mesa-opencl)
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;; This package does not build with either insight-toolkit 5.0.0 and
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;; not with 4.13. It really needs to be 4.12.
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("itk" ,insight-toolkit-4.12)
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("vtk" ,vtk-6)
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("qtbase" ,qtbase)
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("qtdeclarative" ,qtdeclarative)
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("qttools" ,qttools)
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("vxl" ,vxl-1)
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("zlib" ,zlib)))
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(native-inputs
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`(("googletest" ,googletest)
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("pkg-config" ,pkg-config)
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("c3d-src"
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,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3")
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(revision "1")
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(version (git-version "0" revision commit)))
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/pyushkevich/c3d.git")
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(commit commit)))
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(file-name (git-file-name "c3d" version))
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(sha256
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(base32
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"0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3")))))
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;; We are using an arbitrary commit from 2017 because the latest
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;; version breaks the build...
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("greedy-src"
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,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3")
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(revision "1")
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(version (git-version "0" revision commit)))
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/pyushkevich/greedy.git")
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(commit commit)))
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(file-name (git-file-name "greedy" version))
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(sha256
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(base32
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"0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab")))))))
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(home-page "https://sourceforge.net/p/itk-snap/")
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(synopsis "Medical image segmentation")
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(description "ITK-SNAP is a tool for segmenting anatomical structures in
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medical images. It provides an automatic active contour segmentation
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pipeline, along with supporting a manual segmentation toolbox. ITK-SNAP has a
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full-featured UI aimed at clinical researchers.")
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;; This includes the submodules greedy and c3d.
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(license license:gpl3+)))
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