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| -rw-r--r-- | gn/packages/hyphy.scm | 105 |
1 files changed, 105 insertions, 0 deletions
diff --git a/gn/packages/hyphy.scm b/gn/packages/hyphy.scm new file mode 100644 index 0000000..23c0406 --- /dev/null +++ b/gn/packages/hyphy.scm @@ -0,0 +1,105 @@ +;;; 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+)))) + + + |