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-rw-r--r--gnu/packages/bioinformatics.scm109
1 files changed, 109 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9813d07e9c..b122b6d83d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -30,13 +30,17 @@
#:use-module (gnu packages base)
#:use-module (gnu packages compression)
#:use-module (gnu packages java)
+ #:use-module (gnu packages maths)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
#:use-module (gnu packages python)
+ #:use-module (gnu packages statistics)
+ #:use-module (gnu packages swig)
#:use-module (gnu packages tbb)
#:use-module (gnu packages vim)
+ #:use-module (gnu packages xml)
#:use-module (gnu packages zip))
(define-public bedops
@@ -1001,6 +1005,111 @@ sequences.")
;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
(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"))))
+ (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 "-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")