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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+))))
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