From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: Guix <guix-devel@gnu.org>
Subject: [PATCH] Add Shogun.
Date: Wed, 18 Mar 2015 18:00:52 +0100 [thread overview]
Message-ID: <idjzj7ackaj.fsf@bimsb-sys02.mdc-berlin.net> (raw)
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: 0001-gnu-Add-Shogun.patch --]
[-- Type: text/x-patch, Size: 4961 bytes --]
From 083573c250162b9b12173e13e66c04f6c32568fb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
reply other threads:[~2015-03-18 17:01 UTC|newest]
Thread overview: [no followups] expand[flat|nested] mbox.gz Atom feed
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
List information: https://guix.gnu.org/
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=idjzj7ackaj.fsf@bimsb-sys02.mdc-berlin.net \
--to=ricardo.wurmus@mdc-berlin.de \
--cc=guix-devel@gnu.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/guix.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).