From ef781382de7febeec2b4b8f854c88923d9f72e5f Mon Sep 17 00:00:00 2001
From: Dennis E. Mungai
Date: Mon, 29 Feb 2016 22:39:14 +0300
Subject: Added hyphy.scm

Requires a patch or substitute* clause to get working.---
 gn/packages/hyphy.scm | 105 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 105 insertions(+)
 create mode 100644 gn/packages/hyphy.scm

(limited to 'gn')

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+))))
+
+
+
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