Merge branch 'master' of https://github.com/genenetwork/guix-bioinformatics

11 files changed, 606 insertions, 16 deletions

diff --git a/gn/packages/afnumpy.scm b/gn/packages/afnumpy.scm
new file mode 100644
index 0000000..55c05ad
--- /dev/null
+++ b/gn/packages/afnumpy.scm
@@ -0,0 +1,84 @@
+;;; 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 afnumpy)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages attr)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages databases)
+  #:use-module (gnu packages fontutils)
+  #:use-module (gnu packages ghostscript)
+  #:use-module (gnu packages glib)
+  #:use-module (gnu packages gnupg)
+  #:use-module (gnu packages gtk)
+  #:use-module (gnu packages icu4c)
+  #:use-module (gnu packages image)
+  #:use-module (gnu packages libffi)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages multiprecision)
+  #:use-module (gnu packages networking)
+  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages pcre)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages readline)
+  #:use-module (gnu packages statistics)
+  #:use-module (gnu packages texlive)
+  #:use-module (gnu packages texinfo)
+  #:use-module (gnu packages tls)
+  #:use-module (gnu packages web)
+  #:use-module (gnu packages xml)
+  #:use-module (gnu packages xorg)
+  #:use-module (gnu packages zip)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix utils)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
+  #:use-module (guix build-system trivial))
+
+(define-public afnumpy
+(let ((commit "c5594c1"))
+(package
+    (name "afnumpy")
+    (version (string-append "rel1-" commit))
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+              (url "https://github.com/FilipeMaia/afnumpy.git")
+              (commit commit)))
+              (file-name (string-append name "-" commit))
+              (sha256
+               (base32
+                "0n30xn8cz0ww7czb3m6dz5sh87khan7ag3vb192narmxj37l8qy7"))))
+    (build-system python-build-system)
+    ;; (native-inputs
+    ;; `(("python-setuptools" ,python-setuptools)))
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f)) 
+    (home-page "https://github.com/FilipeMaia/afnumpy")
+    (synopsis "Numerical library array processing of numbers, strings, records and objects")
+    (description
+     "A GPGPU-accelerated drop-in of python's numpy")
+    (license license:gpl2)))) 
diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm
index 23ff0af..7756a97 100644
--- a/gn/packages/arrayfire.scm
+++ b/gn/packages/arrayfire.scm
@@ -19,6 +19,7 @@
 (define-module (gn packages arrayfire)
   #:use-module ((guix licenses))
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
   #:use-module (guix packages)
@@ -36,7 +37,6 @@
   #: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)
@@ -44,30 +44,35 @@
   #:use-module (gnu packages linux))
 
 (define-public arrayfire
+(let ((commit "9ca1ea0"))
   (package
     (name "arrayfire")
-    (version "3.3.0")
+    (version "3.3.1-hotfix")
     (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"))
+              (method git-fetch)
+              (uri (git-reference
+              (url "https://github.com/arrayfire/arrayfire.git")
+              (commit commit)))
+              (file-name (string-append name "-" commit))
               (sha256
                (base32
-                "07pbw6vzny3z86y890c0rx7rk31ddchxrrdslk661iq512xppr0g"))))
+                "067y98a9s78vpz7xsg889xnwfaza7c5gdv97yg9cgrdl0iljvsgp"))))
     (native-inputs `(("autoconf" ,autoconf)
         ("automake" ,automake)
         ("cmake" ,cmake)
         ("gawk" ,gawk)
+        ("glew" ,glew)
         ("libtool" ,libtool)
         ("pkg-config" ,pkg-config)))
     (inputs `(("boost" ,boost)
        ("glfw" ,glfw)
        ("curl" ,curl)
+       ("atlas" ,atlas)
        ("dbus" ,dbus)
        ("enca" ,enca)
        ("eudev" ,eudev)
        ("glew" ,glew)
+       ("glib" ,glib)
        ("lapack" ,lapack)
        ("libcap" ,libcap)
        ("libjpeg" ,libjpeg)
@@ -75,7 +80,6 @@
        ("libtiff" ,libtiff)
        ("libyajl" ,libyajl)
        ("mesa-utils" ,mesa-utils)
-       ("mysql" ,mysql)
        ("python" ,python-2)
        ("freeimage" ,freeimage)
        ("fftw" ,fftw)
@@ -88,11 +92,11 @@
        ("cmake" ,cmake)))
     (build-system cmake-build-system)
     (arguments 
-     `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release -DBUILD_OPENCL=ON") #:tests? #f))     
+     `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release" "-DBUILD_OPENCL=OFF" "-DBUILD_GRAPHICS=OFF") #: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+))))
+    (license (list gpl2 gpl2+ gpl3 gpl3+)))))
 
 (define-public glfw
   (package
@@ -111,6 +115,7 @@
         ("automake" ,automake)
         ("cmake" ,cmake)
         ("libtool" ,libtool)
+        ("libpthread-stubs" ,libpthread-stubs)
         ("pkg-config" ,pkg-config)))
     (inputs `(("curl" ,curl)
        ("dbus" ,dbus)
@@ -127,7 +132,6 @@
        ("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.")
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 40dde37..276471b 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -28,6 +28,7 @@
   #:use-module (gnu packages curl)
   #:use-module (gnu packages doxygen)
   #:use-module (gnu packages datastructures)
+  #:use-module (gnu packages check)
   #:use-module (gnu packages file)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 3d62d55..1382cfb 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -150,13 +150,10 @@
                    ;; (url "https://github.com/genenetwork/genenetwork2.git")
                    (url "https://github.com/genenetwork/genenetwork2_diet.git")
                    (commit commit)))
-             (file-name (string-append name "-" (string-take commit 7))) 
+             (file-name (string-append name "-" (string-take commit 7)))
              (sha256
               (base32
                "1zs6jgrpwzxmfjz03whnaw8q6h8f53mycl440p058gfn8x7pd618"))))
-    (inputs `(
-              ("r-wgcna" ,r-wgcna)
-              ("r-qtl" ,r-qtl)))
     (propagated-inputs `(  ;; propagated for development purposes
               ("python" ,python-2) ;; probably superfluous
               ("r" ,r)
diff --git a/gn/packages/glfw.scm b/gn/packages/glfw.scm
new file mode 100644
index 0000000..30342f0
--- /dev/null
+++ b/gn/packages/glfw.scm
@@ -0,0 +1,83 @@
+;;; 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 glfw)
+  #: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 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/llvm.scm b/gn/packages/llvm.scm
new file mode 100644
index 0000000..83ea5d1
--- /dev/null
+++ b/gn/packages/llvm.scm
@@ -0,0 +1,65 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org>
+;;; 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 llvm)
+  #:use-module (guix packages)
+  #:use-module (guix licenses)
+  #:use-module (guix download)
+  #:use-module (guix utils)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system cmake)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages bootstrap)           ;glibc-dynamic-linker
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages xml))
+
+
+(define-public llvm
+(package
+    (name "llvm")
+    (version "3.7.1")
+    (source
+     (origin
+      (method url-fetch)
+      (uri (string-append "http://llvm.org/releases/"
+                          version "/llvm-" version ".src.tar.xz"))
+      (sha256
+       (base32
+        "1masakdp9g2dan1yrazg7md5am2vacbkb3nahb3dchpc1knr8xxy"))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("python" ,python-wrapper)
+       ("perl"   ,perl)))
+    (arguments
+     `(#:configure-flags '("-DCMAKE_SKIP_BUILD_RPATH=FALSE"
+                           "-DCMAKE_BUILD_WITH_INSTALL_RPATH=FALSE")))
+    (home-page "http://www.llvm.org")
+    (synopsis "Optimizing compiler infrastructure")
+    (description
+     "LLVM is a compiler infrastructure designed for compile-time, link-time,
+runtime, and idle-time optimization of programs from arbitrary programming
+languages.  It currently supports compilation of C and C++ programs, using
+front-ends derived from GCC 4.0.1.  A new front-end for the C family of
+languages is in development.  The compiler infrastructure includes mirror sets
+of programming tools as well as libraries with equivalent functionality.")
+    (license license:ncsa)))
diff --git a/gn/packages/ocl-icd.scm b/gn/packages/ocl-icd.scm
new file mode 100644
index 0000000..b33fe9d
--- /dev/null
+++ b/gn/packages/ocl-icd.scm
@@ -0,0 +1,99 @@
+;;; 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 ocl-icd)
+  #:use-module ((guix licenses) #:prefix license:)
+  #: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 ruby)
+  #:use-module (gnu packages zip)
+  #:use-module (gnu packages gnupg)
+  #:use-module (gnu packages bootstrap)
+  #:use-module (guix git-download))
+
+(define-public ocl-icd
+  (package
+   (name "ocl-icd")
+   (version "2.2.9")
+   (source (origin
+             (method url-fetch)
+             (uri (string-append "https://forge.imag.fr/frs/download.php/716/ocl-icd-"
+                                 version ".tar.gz"))
+             (file-name (string-append name "-" version ".tar.gz"))
+             (sha256
+              (base32
+               "1rgaixwnxmrq2aq4kcdvs0yx7i6krakarya9vqs7qwsv5hzc32hc"))))
+    (inputs `(("zip" ,zip)
+             ("autoconf" ,autoconf)
+             ("automake" ,automake)
+             ("ruby" ,ruby)
+             ("libtool" ,libtool)
+             ("opencl-headers" ,opencl-headers)
+             ("libgcrypt" ,libgcrypt)))                                              
+    (build-system gnu-build-system)
+     (arguments
+     '(#:phases (modify-phases %standard-phases
+                    (add-after 'unpack `bootstrap
+                      (lambda _
+                        (zero? (system* "autoreconf" "-vfi")))))))    
+    (home-page "https://forge.imag.fr/projects/ocl-icd/")
+    (synopsis "OpenCL implementations are provided as ICD (Installable Client Driver).")
+    (description "OpenCL implementations are provided as ICD (Installable Client Driver).
+    An OpenCL program can use several ICD thanks to the use of an ICD Loader as provided by this project.
+    This free ICD Loader can load any (free or non free) ICD")
+    (license license:gpl2)))
+    
+    (define-public opencl-headers
+(let ((commit "c1770dc"))
+  (package
+    (name "opencl-headers")
+    (version (string-append "2.1-" commit ))
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+              (url "https://github.com/KhronosGroup/OpenCL-Headers.git")
+              (commit commit)))
+              (file-name (string-append name "-" commit))
+              (sha256
+               (base32
+                "0m9fkblqja0686i2jjqiszvq3df95gp01a2674xknlmkd6525rck"))))
+    (propagated-inputs '())
+    (inputs '())
+    (native-inputs '())
+    (build-system gnu-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'build)
+         (delete 'check)
+         (replace 'install
+                  (lambda* (#:key outputs #:allow-other-keys)
+                    (copy-recursively "." (string-append
+                                                 (assoc-ref outputs "out")
+                                                 "/include/CL")))))))
+    (synopsis "The Khronos OpenCL headers")
+    (description "This package provides the Khronos OpenCL headers")
+    (home-page "https://www.khronos.org/registry/cl/")
+    (license license:gpl2))))
diff --git a/gn/packages/opencl-headers.scm b/gn/packages/opencl-headers.scm
new file mode 100644
index 0000000..bddd136
--- /dev/null
+++ b/gn/packages/opencl-headers.scm
@@ -0,0 +1,63 @@
+;;; 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 opencl-headers)
+  #:use-module ((guix licenses))
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix packages)
+  #:use-module (guix build-system gnu)
+  #:use-module (gnu packages gl)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages xorg)
+  #:use-module (gnu packages version-control)  
+  #:use-module (gnu packages linux))
+
+(define-public opencl-headers
+(let ((commit "c1770dc"))
+  (package
+    (name "opencl-headers")
+    (version (string-append "2.1-" commit ))
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+              (url "https://github.com/KhronosGroup/OpenCL-Headers.git")
+              (commit commit)))
+              (file-name (string-append name "-" commit))
+              (sha256
+               (base32
+                "0m9fkblqja0686i2jjqiszvq3df95gp01a2674xknlmkd6525rck"))))
+    (propagated-inputs '())
+    (inputs '())
+    (native-inputs '())
+    (build-system gnu-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'build)
+         (delete 'check)
+         (replace 'install
+                  (lambda* (#:key outputs #:allow-other-keys)
+                    (copy-recursively "." (string-append
+                                                 (assoc-ref outputs "out")
+                                                 "/include/CL")))))))
+    (synopsis "The Khronos OpenCL headers")
+    (description "This package provides the Khronos OpenCL headers")
+    (home-page "https://www.khronos.org/registry/cl/")
+    (license gpl2))))
diff --git a/gn/packages/opencl-icd-loader.scm b/gn/packages/opencl-icd-loader.scm
new file mode 100644
index 0000000..a8fbc7b
--- /dev/null
+++ b/gn/packages/opencl-icd-loader.scm
@@ -0,0 +1,95 @@
+;;; 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 opencl-icd-loader)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix git-download)
+  #: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 boost)
+  #:use-module (gnu packages gawk)
+  #:use-module (gnu packages cmake)
+  #: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 llvm)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages mpi)
+  #:use-module (gnu packages web)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages xorg)
+  #:use-module (gnu packages version-control)  
+  #:use-module (gnu packages linux))
+
+(define-public opencl-icd-loader
+(let ((commit "bf894eb"))
+  (package
+    (name "opencl-icd-loader")
+    (version (string-append "2.1-" commit ))
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+              (url "https://github.com/KhronosGroup/OpenCL-ICD-Loader.git")
+              (commit commit)))
+              (file-name (string-append name "-" commit))
+              (sha256
+               (base32
+                "1sbxdd9vgl3m8j39kwvvk5cflyj7480pq0s307zg1ssidvj98v3g"))))
+(native-inputs `(("autoconf" ,autoconf)
+                ("automake" ,automake)
+                ("libtool" ,libtool)
+                ("cmake" ,cmake)
+                ("pkg-config" ,pkg-config)))
+(inputs        `(("python" ,python-2)
+               ("boost" ,boost)
+               ("dbus" ,dbus)
+               ("clang" ,clang)
+               ("clang-runtime" ,clang-runtime)
+               ("enca" ,enca)
+               ("eudev" ,eudev)
+               ("fftw-openmpi" ,fftw-openmpi)
+               ("glew" ,glew)
+               ("hwloc" ,hwloc)
+               ("libcap" ,libcap)
+               ("libjpeg" ,libjpeg)
+               ("libltdl" ,libltdl)
+               ("libtiff" ,libtiff)
+               ("llvm" ,llvm)
+               ("mesa-utils" ,mesa-utils)
+               ("openmpi" ,openmpi)
+               ("perl" ,perl)
+               ("randrproto" ,randrproto)
+               ("libxrandr" ,libxrandr)
+               ("xineramaproto" ,xineramaproto)
+               ("libxinerama" ,libxinerama)
+               ("libxcursor" ,libxcursor)
+               ("fftw-openmpi" ,fftw-openmpi)))
+    (build-system cmake-build-system)                
+    (synopsis "The Khronos OpenCL ICDs (Installable Client Driver)")
+    (description "This package provides the Khronos OpenCL ICDs")
+    (home-page "https://www.khronos.org/registry/cl/")
+    (license license:gpl2))))
diff --git a/gn/packages/pocl.scm b/gn/packages/pocl.scm
new file mode 100644
index 0000000..c5cb8cb
--- /dev/null
+++ b/gn/packages/pocl.scm
@@ -0,0 +1,99 @@
+;;; 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 pocl)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix git-download)
+  #:use-module (guix download)
+  #: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 boost)
+  #:use-module (gnu packages gawk)
+  #:use-module (gnu packages cmake)
+  #: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 llvm)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages mpi)
+  #:use-module (gnu packages web)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages xorg)
+  #:use-module (gnu packages version-control)  
+  #:use-module (gnu packages linux))
+
+(define-public pocl
+(let ((commit "a6f377a"))
+  (package
+    (name "pocl")
+    (version (string-append "v09rc-" commit ))
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+              (url "https://github.com/pocl/pocl.git")
+              (commit commit)))
+              (file-name (string-append name "-" commit))
+              (sha256
+               (base32
+                "0b1y8c2y0xx5sqfpkkvgmp02czgmq5immypgm4hhpmp512hcj38j"))))
+(native-inputs `(("autoconf" ,autoconf)
+                ("automake" ,automake)
+                ("libtool" ,libtool)
+                ("cmake" ,cmake)
+                ("pkg-config" ,pkg-config)))
+(inputs        `(("python" ,python-2)
+               ("boost" ,boost)
+               ("dbus" ,dbus)
+               ("clang" ,clang)
+               ("clang-runtime" ,clang-runtime)
+               ("enca" ,enca)
+               ("eudev" ,eudev)
+               ("fftw-openmpi" ,fftw-openmpi)
+               ("glew" ,glew)
+               ("hwloc" ,hwloc)
+               ("libcap" ,libcap)
+               ("libjpeg" ,libjpeg)
+               ("libltdl" ,libltdl)
+               ("libtiff" ,libtiff)
+               ("llvm" ,llvm)
+               ("mesa-utils" ,mesa-utils)
+               ("openmpi" ,openmpi)
+               ("randrproto" ,randrproto)
+               ("libxrandr" ,libxrandr)
+               ("xineramaproto" ,xineramaproto)
+               ("libxinerama" ,libxinerama)
+               ("libxcursor" ,libxcursor)
+               ("fftw-openmpi" ,fftw-openmpi)))
+    (build-system cmake-build-system)
+    (arguments 
+     `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release" "-DBUILD_SHARED_LIBS=ON")
+       #:tests? #f))                
+    (synopsis "pocl: Portable Computing Language (pocl) aims to become a MIT-licensed
+     open source implementation of the OpenCL standard which can be easily adapted for
+     new targets and devices, both for homogeneous CPU and heterogenous GPUs/accelerators.")
+    (description "Portable Computing Language (pocl) aims to become a MIT-licensed
+     open source implementation of the OpenCL standard which can be easily adapted for
+     new targets and devices, both for homogeneous CPU and heterogenous GPUs/accelerators.")
+    (home-page "http://portablecl.org/")
+    (license license:gpl2))))
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 8157c0b..47b2c23 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -355,7 +355,7 @@ project)")
   (description #f)
   (license #f)))
 
-(define-public python2-pil-1.1.6
+(define-public python2-pil
   (package
     (name "python2-pil")
     (version "1.1.6")