Merge branch 'master' of github.com:Brainiarc7/guix-bioinformatics into dennis

3 files changed, 245 insertions, 2 deletions

diff --git a/README.md b/README.md
index 6d8bd0e..a13e0b1 100644
--- a/README.md
+++ b/README.md
@@ -32,7 +32,7 @@ Install slurm with
 
 ## Module system
 
-Install the module envirmonment with
+Install the module environment with
 
     git clone https://github.com/genenetwork/guix-bioinformatics.git
     export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
@@ -44,7 +44,7 @@ Install the module envirmonment with
 
 ## python2-numarray 1.5.2
 
-Install the module envirmonment with
+Install the module environment with
 
     git clone https://github.com/genenetwork/guix-bioinformatics.git
     export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
diff --git a/gn/packages/OpenFYBA b/gn/packages/OpenFYBA
new file mode 100644
index 0000000..5d64381
--- /dev/null
+++ b/gn/packages/OpenFYBA
@@ -0,0 +1,59 @@
+;;; 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 (gnu packages OpenFYBA)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (gnu packages)
+  #: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 bootstrap)
+  #:use-module (guix git-download))
+
+(define-public OpenFYBA
+  (package
+   (name "OpenFYBA")
+   (version "4.4.1")
+   (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 `(("openssl" ,openssl)                                          
+    (build-system gnu-build-system)    
+    (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, distributed by the 
+National Mapping Authority of Norway (Statens kartverk) to read and write 
+files in the National geodata standard format SOSI. 
+The original library has a long history, and was originally developed for 
+systems as diverse as DOS, OS/2-16, OS/2-32, Win16, Win32, and various UNIX 
+variants (POSIX, HPUX, Silicon graphics). In Norwegian. It shows in the 
+source code. OpenFYBA has been tested to run at least on Windows and Linux 
+environments. ")
+    (license license:gpl2+)))
+
diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm
new file mode 100644
index 0000000..1d3401d
--- /dev/null
+++ b/gn/packages/arrayfire.scm
@@ -0,0 +1,184 @@
+;;; 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 (gnu packages arrayfire)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix cmake-build-system)
+  #:use-module (guix licenses)
+  #: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 tls)
+  #:use-module (gnu packages textutils)
+  #:use-module (gnu packages fftw)
+  #:use-module (gnu packages fftw-openmpi)
+  #:use-module (gnu packages fftwf)
+  #:use-module (gnu packages gl)
+  #:use-module (gnu packages glew)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages mesa)
+  #:use-module (gnu packages web)
+  #:use-module (gnu packages linux))
+
+(define-public arrayfire
+  (package
+    (name "arrayfire")
+    (version "v3.3.alpha")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/arrayfire/arrayfire/archive/" version 
+                                  ".tar.gz"))
+              (sha256
+               (base32
+                "0rla0mi5wby8bkpzrj063y6js3d4dlfl3qwfvm8m8skfc21dz52p"))))
+    (build-system cmake-build-system)
+    (arguments `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release -DBUILD_OPENCL=ON")))
+    (native-inputs
+      `(("autoconf" ,autoconf)
+        ("automake" ,automake)
+        ("cmake" ,cmake)
+        ("doxygen" ,doxygen)
+        ("gawk" ,gawk)
+        ("gettext" ,gnu-gettext)
+        ("icedtea7" ,icedtea7) 
+        ("libtool" ,libtool)
+        ("pkg-config" ,pkg-config)
+        ("swig" ,swig)
+        ("which" ,which)
+        ("yasm" ,yasm)))
+    (inputs
+     `(("boost" ,boost)
+       ("bzip2" ,bzip2)
+       ("glfw" ,glfw)
+       ("curl" ,curl)
+       ("dbus" ,dbus)
+       ("enca" ,enca)
+       ("eudev" ,eudev)
+       ("fontconfig" ,fontconfig)
+       ("freetype" ,freetype)
+       ("fribidi" ,fribidi)
+       ("glew" ,glew)
+       ("gnutls" ,gnutls)
+       ("gperf" ,gperf)
+       ("libcap" ,libcap)
+       ("libgcrypt" ,libgcrypt)
+       ("libjpeg" ,libjpeg)
+       ("libltdl" ,libltdl)
+       ("libssh" ,libssh)
+       ("libtiff" ,libtiff)
+       ("libxml2" ,libxml2)
+       ("libxmu" ,libxmu)
+       ("libxrandr" ,libxrandr)
+       ("libxrender" ,libxrender)
+       ("libxslt" ,libxslt)
+       ("libxt" ,libxt)
+       ("libyajl" ,libyajl)
+       ("lzo" ,lzo)
+       ("mesa-utils" ,mesa-utils)
+       ("mysql" ,mysql)
+       ("openssl" ,openssl)
+       ("pcre" ,pcre)
+       ("python" ,python-2)
+       ("tinyxml" ,tinyxml)
+       ("unzip" ,unzip)
+       ("zip" ,zip)
+       ("freeimage" ,freeimage)
+       ("fftw" ,fftw)
+       ("fftwf" ,fftwf)
+       ("fftw-openmpi" ,fftw-openmpi)
+       ("atlas" ,atlas)
+       ("gfortran", gfortran)
+       ("glew" ,glew)
+       ("glu" ,glu)
+       ("libx11" ,libx11)
+       ("libxi" ,libxi)
+       ("libxrandr" ,libxrandr)
+       ("libxxf86vm" ,libxxf86vm)
+       ("inputproto" ,inputproto)
+       ("glproto" ,glproto)
+       ("zlib" ,zlib)))
+    (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 gpl3+)))
+
+(define-public glfw
+  (package
+    (name "glfw")
+    (version "3.0.4")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append "https://github.com/glfw/glfw/archive/"
+                                 version ".zip"))
+             (file-name (string-append name "-" version ".zip"))
+             (sha256
+              (base32
+               "1g0jm80cakk60477zz9z1mpsznxaadsfm318yiigf6kackrkqfqg"))))
+    (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")))
+    (native-inputs
+      `(("autoconf" ,autoconf)
+        ("automake" ,automake)
+        ("cmake" ,cmake)
+        ("libtool" ,libtool)
+        ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("bzip2" ,bzip2)
+       ("curl" ,curl)
+       ("dbus" ,dbus)
+       ("enca" ,enca)
+       ("eudev" ,eudev)
+       ("fontconfig" ,fontconfig)
+       ("freetype" ,freetype)
+       ("fribidi" ,fribidi)
+       ("glew" ,glew)
+       ("gnutls" ,gnutls)
+       ("gperf" ,gperf)
+       ("libcap" ,libcap)
+       ("libgcrypt" ,libgcrypt)
+       ("libjpeg" ,libjpeg)
+       ("libltdl" ,libltdl)
+       ("libssh" ,libssh)
+       ("libtiff" ,libtiff)
+       ("libxml2" ,libxml2)
+       ("libxmu" ,libxmu)
+       ("libxrandr" ,libxrandr)
+       ("libxrender" ,libxrender)
+       ("libxslt" ,libxslt)
+       ("libxt" ,libxt)
+       ("lzo" ,lzo)
+       ("mesa-utils" ,mesa-utils)
+       ("mysql" ,mysql)
+       ("openssl" ,openssl)
+       ("python" ,python-2)
+       ("tinyxml" ,tinyxml)
+       ("unzip" ,unzip)
+       ("zip" ,zip)
+       ("zlib" ,zlib)))
+    (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. It is easy to integrate into existing applications and does not lay claim to the main loop.
+GLFW is written in C and has native support for Windows, OS X and many Unix-like systems using the X Window System, such as Linux and FreeBSD.
+GLFW is licensed under the zlib/libpng license.")
+    (license license:gpl2+)))