mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2024-12-26 22:38:07 -05:00
c1670a8196
* gnu/packages/bioinformatics.scm (shogun): Move from here... * gnu/packages/machine-learning.scm (shogun): ...to here.
289 lines
12 KiB
Scheme
289 lines
12 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
|
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
|
|
;;;
|
|
;;; This file is part of GNU Guix.
|
|
;;;
|
|
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
|
;;; under the terms of the GNU General Public License as published by
|
|
;;; the Free Software Foundation; either version 3 of the License, or (at
|
|
;;; your option) any later version.
|
|
;;;
|
|
;;; GNU Guix is distributed in the hope that it will be useful, but
|
|
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
;;; GNU General Public License for more details.
|
|
;;;
|
|
;;; You should have received a copy of the GNU General Public License
|
|
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
|
|
|
(define-module (gnu packages machine-learning)
|
|
#:use-module ((guix licenses) #:prefix license:)
|
|
#:use-module (guix packages)
|
|
#:use-module (guix utils)
|
|
#:use-module (guix download)
|
|
#:use-module (guix build-system cmake)
|
|
#:use-module (guix build-system gnu)
|
|
#:use-module (gnu packages)
|
|
#:use-module (gnu packages boost)
|
|
#:use-module (gnu packages compression)
|
|
#:use-module (gnu packages gcc)
|
|
#:use-module (gnu packages maths)
|
|
#:use-module (gnu packages pkg-config)
|
|
#:use-module (gnu packages python)
|
|
#:use-module (gnu packages statistics)
|
|
#:use-module (gnu packages swig)
|
|
#:use-module (gnu packages xml))
|
|
|
|
(define-public libsvm
|
|
(package
|
|
(name "libsvm")
|
|
(version "3.20")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"https://github.com/cjlin1/libsvm/archive/v"
|
|
(string-delete #\. version) ".tar.gz"))
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1jpjlql3frjza7zxzrqqr2firh44fjb8fqsdmvz6bjz7sb47zgp4"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:tests? #f ;no "check" target
|
|
#:phases (modify-phases %standard-phases
|
|
(delete 'configure)
|
|
(replace
|
|
'install
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
(bin (string-append out "/bin/")))
|
|
(mkdir-p bin)
|
|
(for-each (lambda (file)
|
|
(copy-file file (string-append bin file)))
|
|
'("svm-train"
|
|
"svm-predict"
|
|
"svm-scale")))
|
|
#t)))))
|
|
(home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
|
|
(synopsis "Library for Support Vector Machines")
|
|
(description
|
|
"LIBSVM is a machine learning library for support vector
|
|
classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
|
|
distribution estimation (one-class SVM). It supports multi-class
|
|
classification.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-libsvm
|
|
(package (inherit libsvm)
|
|
(name "python-libsvm")
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:tests? #f ;no "check" target
|
|
#:make-flags '("-C" "python")
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(delete 'configure)
|
|
(replace
|
|
'install
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(let ((site (string-append (assoc-ref outputs "out")
|
|
"/lib/python"
|
|
(string-take
|
|
(string-take-right
|
|
(assoc-ref inputs "python") 5) 3)
|
|
"/site-packages/")))
|
|
(substitute* "python/svm.py"
|
|
(("../libsvm.so.2") "libsvm.so.2"))
|
|
(mkdir-p site)
|
|
(for-each (lambda (file)
|
|
(copy-file file (string-append site (basename file))))
|
|
(find-files "python" "\\.py"))
|
|
(copy-file "libsvm.so.2"
|
|
(string-append site "libsvm.so.2")))
|
|
#t)))))
|
|
(inputs
|
|
`(("python" ,python)))
|
|
(synopsis "Python bindings of libSVM")))
|
|
|
|
(define-public randomjungle
|
|
(package
|
|
(name "randomjungle")
|
|
(version "2.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"http://www.imbs-luebeck.de/imbs/sites/default/files/u59/"
|
|
"randomjungle-" version ".tar_.gz"))
|
|
(sha256
|
|
(base32
|
|
"12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:configure-flags
|
|
(list (string-append "--with-boost="
|
|
(assoc-ref %build-inputs "boost")))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-before
|
|
'configure 'set-CXXFLAGS
|
|
(lambda _
|
|
(setenv "CXXFLAGS" "-fpermissive ")
|
|
#t)))))
|
|
(inputs
|
|
`(("boost" ,boost)
|
|
("gsl" ,gsl)
|
|
("libxml2" ,libxml2)
|
|
("zlib" ,zlib)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "http://www.imbs-luebeck.de/imbs/de/node/227/")
|
|
(synopsis "Implementation of the Random Forests machine learning method")
|
|
(description
|
|
"Random Jungle is an implementation of Random Forests. It is supposed to
|
|
analyse high dimensional data. In genetics, it can be used for analysing big
|
|
Genome Wide Association (GWA) data. Random Forests is a powerful machine
|
|
learning method. Most interesting features are variable selection, missing
|
|
value imputation, classifier creation, generalization error estimation and
|
|
sample proximities between pairs of cases.")
|
|
(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+)))
|