Merge pull request #6 from Brainiarc7/master

Update this fork with Pjotr's upstream code.

3 files changed, 302 insertions, 0 deletions

diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm
new file mode 100644
index 0000000..23ff0af
--- /dev/null
+++ b/gn/packages/arrayfire.scm
@@ -0,0 +1,136 @@
+;;; 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 arrayfire)
+  #: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 ldc)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages xorg)
+  #:use-module (gnu packages version-control)  
+  #:use-module (gnu packages linux))
+
+(define-public arrayfire
+  (package
+    (name "arrayfire")
+    (version "3.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://arrayfire.com/arrayfire_source/arrayfire-full-" version 
+                                  ".tar.bz2"))
+              (file-name (string-append name "-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "07pbw6vzny3z86y890c0rx7rk31ddchxrrdslk661iq512xppr0g"))))
+    (native-inputs `(("autoconf" ,autoconf)
+        ("automake" ,automake)
+        ("cmake" ,cmake)
+        ("gawk" ,gawk)
+        ("libtool" ,libtool)
+        ("pkg-config" ,pkg-config)))
+    (inputs `(("boost" ,boost)
+       ("glfw" ,glfw)
+       ("curl" ,curl)
+       ("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 
+     `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release -DBUILD_OPENCL=ON") #:tests? #f))     
+    (synopsis "ArrayFire: a general purpose GPU library. https://arrayfire.com")
+    (description "ArrayFire is a high performance software library for parallel computing with an easy-to-use API. Its array based function set makes parallel programming simple.")
+    (home-page "http://arrayfire.com/")
+    (license (list gpl2 gpl2+ gpl3 gpl3+))))
+
+(define-public glfw
+  (package
+    (name "glfw")
+    (version "3.1.2")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append "https://github.com/glfw/glfw/archive/"
+                                 version ".tar.gz"))
+             (sha256
+              (base32
+               "08pixv8hd5xsccf7l8cqcijjqaq4k4da8qbp77wggal2fq445ika"))))
+    (build-system cmake-build-system)
+    (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON") #:tests? #f))
+    (native-inputs `(("autoconf" ,autoconf)
+        ("automake" ,automake)
+        ("cmake" ,cmake)
+        ("libtool" ,libtool)
+        ("pkg-config" ,pkg-config)))
+    (inputs `(("curl" ,curl)
+       ("dbus" ,dbus)
+       ("enca" ,enca)
+       ("eudev" ,eudev)
+       ("glew" ,glew)
+       ("libcap" ,libcap)
+       ("libjpeg" ,libjpeg)
+       ("libltdl" ,libltdl)
+       ("libtiff" ,libtiff)
+       ("mesa-utils" ,mesa-utils)
+       ("randrproto" ,randrproto)
+       ("libxrandr" ,libxrandr)
+       ("xineramaproto" ,xineramaproto)
+       ("libxinerama" ,libxinerama)
+       ("libxcursor" ,libxcursor)
+       ("mysql" ,mysql)
+       ("python" ,python-2)))       
+    (home-page "http://www.glfw.org/")
+    (synopsis "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.")
+    (description "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.")
+    (license (list gpl2))))
+
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+))))
+
+
+
diff --git a/gn/packages/openfyba.scm b/gn/packages/openfyba.scm
new file mode 100644
index 0000000..2b20d09
--- /dev/null
+++ b/gn/packages/openfyba.scm
@@ -0,0 +1,61 @@
+;;; 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 openfyba)
+  #:use-module ((guix licenses))
+  #:use-module (gnu packages)
+  #:use-module (gnu packages autotools)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix build-system gnu)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages textutils)
+  #:use-module (gnu packages base)
+  ;;#:use-module (gnu packages tls)
+  #:use-module (gnu packages zip)
+  #:use-module (gnu packages gnupg)
+  #:use-module (gnu packages bootstrap)
+  #:use-module (guix git-download))
+
+(define-public openfyba
+  (package
+   (name "openfyba")
+   (version "4.1.1")
+   (source (origin
+             (method url-fetch)
+             (uri (string-append "https://github.com/kartverket/fyba/archive/"
+                                 version ".tar.gz"))
+             (file-name (string-append name "-" version ".tar.gz"))
+             (sha256
+              (base32
+               "0ya1agi78d386skq353dk400fl11q6whfqmv31qrkn4g5vamixlr"))))
+    (inputs `(("zip" ,zip)
+             ("autoconf" ,autoconf)
+             ("automake" ,automake)
+             ("libtool" ,libtool)
+             ("libgcrypt" ,libgcrypt)))                                              
+    (build-system gnu-build-system)
+     (arguments
+     '(#:phases (modify-phases %standard-phases
+                    (add-after 'unpack `bootstrap
+                      (lambda _
+                        (zero? (system* "autoreconf" "-vfi")))))))    
+    (home-page "http://labs.kartverket.no/sos/")
+    (synopsis "source code release of the FYBA library")
+    (description "OpenFYBA is the source code release of the FYBA library.")
+    (license (list gpl2))))