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-rw-r--r--gn/packages/hyphy.scm105
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+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com>
+;;;
+;;; 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 (gn packages hyphy)
+ #:use-module ((guix licenses))
+ #:use-module (guix download)
+ #:use-module (guix build-system gnu)
+ #:use-module (guix build-system cmake)
+ #:use-module (guix packages)
+ #:use-module (gnu packages algebra)
+ #:use-module (gnu packages autotools)
+ #:use-module (gnu packages curl)
+ #:use-module (gnu packages gawk)
+ #:use-module (gnu packages cmake)
+ #:use-module (gnu packages boost)
+ #:use-module (gnu packages glib)
+ #:use-module (gnu packages image)
+ #:use-module (gnu packages video)
+ #:use-module (gnu packages textutils)
+ #:use-module (gnu packages gl)
+ #:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages maths)
+ #:use-module (gnu packages web)
+ #:use-module (gnu packages databases)
+ #:use-module (gnu packages python)
+ #:use-module (gnu packages xorg)
+ #:use-module (gnu packages version-control)
+ #:use-module (gnu packages linux))
+
+(define-public hyphy
+ (package
+ (name "hyphy")
+ (version "2.2.6")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/veg/hyphy/archive/" version
+ ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "00i3609nywb1xfq50p3kvfbvahql241ciq23jrf67z0yp4y5l5a9"))))
+ (native-inputs `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("cmake" ,cmake)
+ ("gawk" ,gawk)
+ ("libtool" ,libtool)
+ ("pkg-config" ,pkg-config)))
+ (inputs `(("boost" ,boost)
+ ("curl" ,curl)
+ ("atlas" ,atlas)
+ ("dbus" ,dbus)
+ ("enca" ,enca)
+ ("eudev" ,eudev)
+ ("glew" ,glew)
+ ("lapack" ,lapack)
+ ("libcap" ,libcap)
+ ("libjpeg" ,libjpeg)
+ ("libltdl" ,libltdl)
+ ("libtiff" ,libtiff)
+ ("libyajl" ,libyajl)
+ ("mesa-utils" ,mesa-utils)
+ ("mysql" ,mysql)
+ ("python" ,python-2)
+ ("freeimage" ,freeimage)
+ ("fftw" ,fftw)
+ ("fftwf" ,fftwf)
+ ("fftw-openmpi" ,fftw-openmpi)
+ ("glew" ,glew)
+ ("glu" ,glu)
+ ("openblas" ,openblas)
+ ("git" ,git)
+ ("cmake" ,cmake)))
+ (build-system cmake-build-system)
+ (arguments
+ '(#:phases (modify-phases %standard-phases
+ (add-after 'unpack `bootstrap
+ (lambda _
+ (zero? (system* "make" "MPI")))))))
+ (arguments
+ `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release") #:tests? #f))
+ (synopsis "hyphy: an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.")
+ (description "HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.
+ It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for
+ parallel computing environments (via message passing interface (MPI)) and it can be compiled as a shared library and called from other programming environments such as
+ Python and R. ")
+ (home-page "http://hyphy.org")
+ (license (list gpl2 gpl2+ gpl3 gpl3+))))
+
+
+