diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 140 |
1 files changed, 0 insertions, 140 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 06037c1bbf..7a50a85f2d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -46,7 +46,6 @@ #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages statistics) - #:use-module (gnu packages swig) #:use-module (gnu packages tbb) #:use-module (gnu packages textutils) #:use-module (gnu packages vim) @@ -2476,145 +2475,6 @@ features; exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.") (license license:gpl3+))) -(define-public shogun - (package - (name "shogun") - (version "4.0.0") - (source - (origin - (method url-fetch) - (uri (string-append - "ftp://shogun-toolbox.org/shogun/releases/" - (version-major+minor version) - "/sources/shogun-" version ".tar.bz2")) - (sha256 - (base32 - "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb")) - (modules '((guix build utils) - (ice-9 rdelim))) - (snippet - '(begin - ;; Remove non-free sources and files referencing them - (for-each delete-file - (find-files "src/shogun/classifier/svm/" - "SVMLight\\.(cpp|h)")) - (for-each delete-file - (find-files "examples/undocumented/libshogun/" - (string-append - "(classifier_.*svmlight.*|" - "evaluation_cross_validation_locked_comparison).cpp"))) - ;; Remove non-free functions. - (define (delete-ifdefs file) - (with-atomic-file-replacement file - (lambda (in out) - (let loop ((line (read-line in 'concat)) - (skipping? #f)) - (if (eof-object? line) - #t - (let ((skip-next? - (or (and skipping? - (not (string-prefix? - "#endif //USE_SVMLIGHT" line))) - (string-prefix? - "#ifdef USE_SVMLIGHT" line)))) - (when (or (not skipping?) - (and skipping? (not skip-next?))) - (display line out)) - (loop (read-line in 'concat) skip-next?))))))) - (for-each delete-ifdefs (find-files "src/shogun/kernel/" - "^Kernel\\.(cpp|h)")))))) - (build-system cmake-build-system) - (arguments - '(#:tests? #f ;no check target - #:phases - (alist-cons-after - 'unpack 'delete-broken-symlinks - (lambda _ - (for-each delete-file '("applications/arts/data" - "applications/asp/data" - "applications/easysvm/data" - "applications/msplicer/data" - "applications/ocr/data" - "examples/documented/data" - "examples/documented/matlab_static" - "examples/documented/octave_static" - "examples/undocumented/data" - "examples/undocumented/matlab_static" - "examples/undocumented/octave_static" - "tests/integration/data" - "tests/integration/matlab_static" - "tests/integration/octave_static" - "tests/integration/python_modular/tests")) - #t) - (alist-cons-after - 'unpack 'change-R-target-path - (lambda* (#:key outputs #:allow-other-keys) - (substitute* '("src/interfaces/r_modular/CMakeLists.txt" - "src/interfaces/r_static/CMakeLists.txt" - "examples/undocumented/r_modular/CMakeLists.txt") - (("\\$\\{R_COMPONENT_LIB_PATH\\}") - (string-append (assoc-ref outputs "out") - "/lib/R/library/"))) - #t) - (alist-cons-after - 'unpack 'fix-octave-modules - (lambda* (#:key outputs #:allow-other-keys) - (substitute* '("src/interfaces/octave_modular/CMakeLists.txt" - "src/interfaces/octave_static/CMakeLists.txt") - (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}") - "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")) - - ;; change target directory - (substitute* "src/interfaces/octave_modular/CMakeLists.txt" - (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}") - (string-append (assoc-ref outputs "out") - "/share/octave/packages"))) - #t) - (alist-cons-before - 'build 'set-HOME - ;; $HOME needs to be set at some point during the build phase - (lambda _ (setenv "HOME" "/tmp") #t) - %standard-phases)))) - #:configure-flags - (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE" - "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT - ;;"-DJavaModular=ON" ;requires unpackaged jblas - ;;"-DRubyModular=ON" ;requires unpackaged ruby-narray - ;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist - ;;"-DLuaModular=ON" ;fails because lua doesn't build pkgconfig file - "-DOctaveModular=ON" - "-DOctaveStatic=ON" - "-DPythonModular=ON" - "-DPythonStatic=ON" - "-DRModular=ON" - "-DRStatic=ON" - "-DCmdLineStatic=ON"))) - (inputs - `(("python" ,python) - ("numpy" ,python-numpy) - ("r" ,r) - ("octave" ,octave) - ("swig" ,swig) - ("hdf5" ,hdf5) - ("atlas" ,atlas) - ("arpack" ,arpack-ng) - ("lapack" ,lapack) - ("glpk" ,glpk) - ("libxml2" ,libxml2) - ("lzo" ,lzo) - ("zlib" ,zlib))) - (native-inputs - `(("pkg-config" ,pkg-config))) - (home-page "http://shogun-toolbox.org/") - (synopsis "Machine learning toolbox") - (description - "The Shogun Machine learning toolbox provides a wide range of unified and -efficient Machine Learning (ML) methods. The toolbox seamlessly allows to -combine multiple data representations, algorithm classes, and general purpose -tools. This enables both rapid prototyping of data pipelines and extensibility -in terms of new algorithms.") - (license license:gpl3+))) - (define-public vcftools (package (name "vcftools") |