From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add Shogun. Date: Wed, 18 Mar 2015 18:00:52 +0100 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:37992) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YYHL8-0006Le-Ap for guix-devel@gnu.org; Wed, 18 Mar 2015 13:01:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YYHL3-00059g-Cm for guix-devel@gnu.org; Wed, 18 Mar 2015 13:01:06 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:34761) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YYHL2-00059R-Vd for guix-devel@gnu.org; Wed, 18 Mar 2015 13:01:01 -0400 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 1284B3806EF for ; Wed, 18 Mar 2015 18:00:59 +0100 (CET) Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 8TZNhwdyBd1u for ; Wed, 18 Mar 2015 18:00:53 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Wed, 18 Mar 2015 18:00:53 +0100 (CET) Content-Disposition: inline; filename="0001-gnu-Add-Shogun.patch" List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Guix >From 083573c250162b9b12173e13e66c04f6c32568fb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Mar 2015 17:59:20 +0100 Subject: [PATCH] gnu: Add Shogun. * gnu/packages/bioinformatics.scm (shogun): New variable. --- gnu/packages/bioinformatics.scm | 92 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 92 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e4017d2..1bf6ad5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -28,12 +28,16 @@ #: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 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 @@ -900,3 +904,91 @@ chimeric (fusion) transcripts, and is also capable of mapping full-length RNA 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/4.0/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"))) + (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/")))) + (alist-cons-before + 'build 'set-HOME + ;; $HOME needs to be set at some point during the build phase + (lambda _ (setenv "HOME" "/tmp")) + %standard-phases))) + #:configure-flags + (list "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT + "-DPythonModular=ON" + "-DPythonStatic=ON" + "-DRModular=ON" + "-DRStatic=ON" + "-DCmdLineStatic=ON" + ;;"-DJavaModular=ON" + ;;"-DLuaModular=ON" + ;;"-DOctaveModular=ON" + ;;"-DOctaveStatic=ON" + ;;"-DPerlModular=ON" + ;;"-DRubyModular=ON" + ))) + (inputs + `(("python" ,python) + ("numpy" ,python-numpy) + ("r" ,r) + ("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+))) -- 2.1.0