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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com>
;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; 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) #:prefix license:)
#:use-module (guix git-download)
#:use-module (guix build-system cmake)
#:use-module (guix packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages curl)
#:use-module (gnu packages mpi)
#:use-module (gnu packages python)
#:use-module (gnu packages tls))
;; TODO: Unbundle sqlite, gtest
(define-public hyphy ; guix: check
(package
(name "hyphy")
(version "2.5.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/veg/hyphy.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1fvmwg2rxkz3abhhldiir69vmyc4i85vdvy64bizgxd0g2k2bikm"))))
(inputs
`(("curl" ,curl)
("fftw-openmpi" ,fftw-openmpi)
("openmpi" ,openmpi)
("openssl" ,openssl)
("python" ,python-2)))
(build-system cmake-build-system)
(arguments
'(#:make-flags '("MPI") ; Add "GTEST" for tests, currently fails to compile.
#:configure-flags (list "-DCMAKE_BUILD_TYPE=Release"
(string-append "-DINSTALL_PREFIX="
(assoc-ref %outputs "out")))
#:tests? #f
#:test-target "HYPHYGTEST"))
(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 license:expat)))
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