gn: Remove some duplicate packages

8 files changed, 11 insertions, 748 deletions

diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm
index 39e7899..c230dc4 100644
--- a/gn/packages/arrayfire.scm
+++ b/gn/packages/arrayfire.scm
@@ -52,7 +52,10 @@
   #:use-module (gnu packages ruby)
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages version-control)
-  #:use-module (gnu packages linux))
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages opencl)
+  #:use-module (gn packages ocl-headers)
+  #:use-module (gn packages ocl-icd))
 
 (define-public arrayfire
 (package
@@ -292,69 +295,3 @@
     (synopsis "Peer-reviewed portable C++ source libraries,BoostCompute")
     (description "Peer-reviewed portable C++ source libraries,BoostCompute")
     (license (list license:x11-style))))
-
-(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 (list license:gpl2 license:ruby))))
-
-(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 (list license:gpl2)))))
diff --git a/gn/packages/beignet.scm b/gn/packages/beignet.scm
index c07fa61..ea099c4 100644
--- a/gn/packages/beignet.scm
+++ b/gn/packages/beignet.scm
@@ -47,7 +47,10 @@
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages version-control)
-  #:use-module (gnu packages linux))
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages opencl)
+  #:use-module (gn packages ocl-headers)
+  #:use-module (gn packages ocl-icd))
 
 (define-public beignet
   (package
@@ -87,69 +90,3 @@
     (synopsis "Intel's OpenCL framework")
     (description "Intel's OpenCL framework that works with Intel IvyBridge GPUs and above")
     (license license:gpl2)))
-
-(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/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 5ee126e..e5914c2 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -431,7 +431,7 @@ automatically handles index file generation and use.")
       ;; A part of the program is licensed GPLv2.
       (license (list license:non-copyleft license:gpl2)))))
 
-(define-public vcflib ; guix duplicat, see below?
+(define-public vcflib
   (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
     (package
       (name "vcflib")
@@ -808,135 +808,6 @@ integration with gPLINK and Haploview, there is some support for the
 subsequent visualization, annotation and storage of results.")
     (license license:gpl3+))))
 
-
-(define-public vcflib ; duplicate? See above
-  (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
-    (package
-      (name "vcflib")
-      (version (string-append "v1.0.2-" (string-take commit 7)))
-      (source
-       (origin
-         (method url-fetch)
-         (uri (string-append "https://github.com/vcflib/vcflib/archive/"
-                "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92" ".tar.gz"))
-         (file-name "vcflib-5ac0913.tar.gz")
-         (sha256
-          (base32 "0ywshwpif059z5h0g7zzrdfzzdj2gr8xvwlwcsdxrms3p9iy35h8"))))
-      (build-system gnu-build-system)
-      (native-inputs
-       `(("htslib" ,htslib)
-         ("zlib" ,zlib)
-         ("python" ,python-2)
-         ("perl" ,perl)
-         ("tabixpp-src"
-          ,(origin
-            (method url-fetch)
-            (uri (string-append "https://github.com/ekg/tabixpp/archive/"
-                  "bbc63a49acc52212199f92e9e3b8fba0a593e3f7" ".tar.gz"))
-            (file-name "tabixpp-src.tar.gz")
-            (sha256
-             (base32 "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77"))))
-         ("intervaltree-src"
-          ,(origin
-             (method url-fetch)
-             (uri (string-append
-                   "https://github.com/ekg/intervaltree/archive/"
-                   "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz"))
-             (file-name "intervaltree-src.tar.gz")
-             (sha256
-              (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks"))))
-         ("smithwaterman-src"
-          ,(origin
-            (method url-fetch)
-            (uri (string-append "https://github.com/ekg/smithwaterman/archive/"
-                  "203218b47d45ac56ef234716f1bd4c741b289be1" ".tar.gz"))
-            (file-name "smithwaterman-src.tar.gz")
-            (sha256
-             (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b"))))
-         ("multichoose-src"
-          ,(origin
-            (method url-fetch)
-            (uri (string-append "https://github.com/ekg/multichoose/archive/"
-                  "73d35daa18bf35729b9ba758041a9247a72484a5" ".tar.gz"))
-            (file-name "multichoose-src.tar.gz")
-            (sha256
-             (base32 "07aizwdabmlnjaq4p3v0vsasgz1xzxid8xcxcw3paq8kh9c1099i"))))
-         ("fsom-src"
-          ,(origin
-            (method url-fetch)
-            (uri (string-append "https://github.com/ekg/fsom/archive/"
-                  "a6ef318fbd347c53189384aef7f670c0e6ce89a3" ".tar.gz"))
-            (file-name "fsom-src.tar.gz")
-            (sha256
-             (base32 "0q6b57ppxfvsm5cqmmbfmjpn5qvx2zi5pamvp3yh8gpmmz8cfbl3"))))
-         ("filevercmp-src"
-          ,(origin
-            (method url-fetch)
-            (uri (string-append "https://github.com/ekg/filevercmp/archive/"
-                  "1a9b779b93d0b244040274794d402106907b71b7" ".tar.gz"))
-            (file-name "filevercmp-src.tar.gz")
-            (sha256
-             (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
-         ("fastahack-src"
-          ,(origin
-            (method url-fetch)
-            (uri (string-append "https://github.com/ekg/fastahack/archive/"
-                  "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd" ".tar.gz"))
-            (file-name "fastahack-src.tar.gz")
-            (sha256
-             (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2"))))))
-      (arguments
-       `(#:tests? #f
-         #:phases
-         (modify-phases %standard-phases
-           (delete 'configure)
-           (delete 'check)
-           (add-after 'unpack 'unpack-submodule-sources
-             (lambda* (#:key inputs #:allow-other-keys)
-               (let ((unpack (lambda (source target)
-                               (with-directory-excursion target
-                                 (zero? (system* "tar" "xvf"
-                                        (assoc-ref inputs source)
-                                        "--strip-components=1"))))))
-                 (and
-                  (unpack "intervaltree-src" "intervaltree")
-                  (unpack "fastahack-src" "fastahack")
-                  (unpack "filevercmp-src" "filevercmp")
-                  (unpack "fsom-src" "fsom")
-                  (unpack "intervaltree-src" "intervaltree")
-                  (unpack "multichoose-src" "multichoose")
-                  (unpack "smithwaterman-src" "smithwaterman")
-                  (unpack "tabixpp-src" "tabixpp")))))
-           (add-after 'unpack-submodule-sources 'fix-makefile
-             (lambda* (#:key inputs #:allow-other-keys)
-               (substitute* '("Makefile")
-                 (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0"))))
-           (replace
-            'build
-            (lambda* (#:key inputs make-flags #:allow-other-keys)
-              (with-directory-excursion "tabixpp"
-                (zero? (system* "make")))
-              (zero? (system* "make" "CC=gcc"
-                (string-append "CFLAGS=\"" "-Itabixpp "
-                  "-I" (assoc-ref inputs "htslib") "/include " "\"") "all"))))
-           (replace
-            'install
-            (lambda* (#:key outputs #:allow-other-keys)
-              (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
-                    (lib (string-append (assoc-ref outputs "out") "/lib")))
-                (for-each (lambda (file)
-                           (install-file file bin))
-                         (find-files "bin" ".*"))
-                (install-file "libvcflib.a" lib)))))))
-      (home-page "https://github.com/vcflib/vcflib/")
-      (synopsis "Library for parsing and manipulating VCF files")
-      (description "Vcflib provides methods to manipulate and interpret
-sequence variation as it can be described by VCF. It is both an API for parsing
-and operating on records of genomic variation as it can be described by the VCF
-format, and a collection of command-line utilities for executing complex
-manipulations on VCF files.")
-      (license license:expat))))
-
 (define-public pindel
   (package
    (name "pindel")
diff --git a/gn/packages/clBLAS.scm b/gn/packages/clBLAS.scm
deleted file mode 100644
index 1c838fb..0000000
--- a/gn/packages/clBLAS.scm
+++ /dev/null
@@ -1,162 +0,0 @@
-;;; 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 clBLAS)
-  #:use-module ((guix licenses) #:prefix license:)
-  #: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)
-  #:use-module (gnu packages algebra)
-  #:use-module (gnu packages autotools)
-  #:use-module (gnu packages bootstrap)
-  #:use-module (gnu packages base)
-  #:use-module (gnu packages curl)
-  #:use-module (gnu packages compression)
-  #: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 gcc)
-  #:use-module (gnu packages gnupg)
-  #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages maths)
-  #:use-module (gnu packages mpi)
-  #:use-module (gnu packages ruby)
-  #: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 clBLAS
-  (package
-    (name "clBLAS")
-    (version "v2.10")
-    (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/clMathLibraries/clBLAS/archive/"
-                                 version ".tar.gz"))
-             (sha256
-              (base32
-               "0adlb02lqzrklfybhnv4n0p37mvkvdi3vqiwa05x2mv05ywnr93j"))))
-    (build-system cmake-build-system)
-    (arguments `(#:tests? #f
-                 #:configure-flags '("../clBLAS-2.10/src" "-DBUILD_SHARED_LIBS=ON" "-DCMAKE_BUILD_TYPE=Release" "-DBUILD_TEST=OFF")))
-    (native-inputs `(("autoconf" ,autoconf)
-        ("automake" ,automake)
-        ("cmake" ,cmake)
-        ("gfortran" ,gfortran)
-        ("libtool" ,libtool)
-        ("pkg-config" ,pkg-config)))
-    (inputs `(("curl" ,curl)
-       ("dbus" ,dbus)
-       ("boost" ,boost)
-       ("enca" ,enca)
-       ("eudev" ,eudev)
-       ("fftw-openmpi" ,fftw-openmpi)
-       ("glew" ,glew)
-       ("libcap" ,libcap)
-       ("libjpeg" ,libjpeg)
-       ("libltdl" ,libltdl)
-       ("libtiff" ,libtiff)
-       ("mesa-utils" ,mesa-utils)
-       ("openmpi" ,openmpi)
-       ("ocl-icd" ,ocl-icd)
-       ("opencl-headers" ,opencl-headers)
-       ("randrproto" ,randrproto)
-       ("libxrandr" ,libxrandr)
-       ("xineramaproto" ,xineramaproto)
-       ("libxinerama" ,libxinerama)
-       ("libxcursor" ,libxcursor)
-       ("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 license:gpl2))))
-
-(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 (list license:gpl2 license:ruby))))
-
-(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 (list license:gpl2)))))
diff --git a/gn/packages/clFFT.scm b/gn/packages/clFFT.scm
deleted file mode 100644
index fb42c85..0000000
--- a/gn/packages/clFFT.scm
+++ /dev/null
@@ -1,158 +0,0 @@
-;;; 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 clFFT)
-  #:use-module ((guix licenses) #:prefix license:)
-  #: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)
-  #:use-module (gnu packages algebra)
-  #:use-module (gnu packages bootstrap)
-  #:use-module (gnu packages base)
-  #:use-module (gnu packages autotools)
-  #:use-module (gnu packages compression)
-  #: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 gnupg)
-  #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages maths)
-  #:use-module (gnu packages mpi)
-  #:use-module (gnu packages ruby)
-  #: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 clFFT
-  (package
-    (name "clFFT")
-    (version "v2.10.1")
-    (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/clMathLibraries/clFFT/archive/"
-                                 version ".tar.gz"))
-             (sha256
-              (base32
-               "19hrk1lf06kch8x9dpbdj0waycn2mldrmj2y4vzi7zn2gdfw6g73"))))
-    (build-system cmake-build-system)
-    (arguments `(#:configure-flags '("../clFFT-2.10.1/src" "-DBUILD_SHARED_LIBS=ON" "-DCMAKE_BUILD_TYPE=Release") #: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)
-       ("fftw-openmpi" ,fftw-openmpi)
-       ("glew" ,glew)
-       ("libcap" ,libcap)
-       ("libjpeg" ,libjpeg)
-       ("libltdl" ,libltdl)
-       ("libtiff" ,libtiff)
-       ("mesa-utils" ,mesa-utils)
-       ("openmpi" ,openmpi)
-       ("ocl-icd" ,ocl-icd)
-       ("opencl-headers" ,opencl-headers)
-       ("randrproto" ,randrproto)
-       ("libxrandr" ,libxrandr)
-       ("xineramaproto" ,xineramaproto)
-       ("libxinerama" ,libxinerama)
-       ("libxcursor" ,libxcursor)
-       ("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 license:gpl2))))
-
-(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 (list license:gpl2 license:ruby))))
-
-(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 (list license:gpl2)))))
diff --git a/gn/packages/glfw.scm b/gn/packages/glfw.scm
deleted file mode 100644
index 6eb3a75..0000000
--- a/gn/packages/glfw.scm
+++ /dev/null
@@ -1,83 +0,0 @@
-;;; 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 ; guix opengl
-  (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/ocl-icd.scm b/gn/packages/ocl-icd.scm
index 79b4853..17e85d7 100644
--- a/gn/packages/ocl-icd.scm
+++ b/gn/packages/ocl-icd.scm
@@ -30,6 +30,8 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages ruby)
+  #:use-module (gnu packages opencl)
+  #:use-module (gn packages ocl-headers)
   #:use-module (guix git-download))
 
 (define-public ocl-icd
@@ -63,37 +65,3 @@
     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/ruby.scm b/gn/packages/ruby.scm
index e46616c..8dfb1d2 100644
--- a/gn/packages/ruby.scm
+++ b/gn/packages/ruby.scm
@@ -292,53 +292,6 @@ a history.")
     "https://github.com/pjotrp/bioruby-logger-plugin")
   (license #f)))
 
-(define-public bio-table ; guix maybe ready
-(package
-  (name "bio-table")
-  (version "1.0.0")
-  (source
-    (origin
-      (method url-fetch)
-      (uri (rubygems-uri "bio-table" version))
-      (sha256
-        (base32
-          "1jlpls734kd41rffn2y2747nr14k5rwgaj2g3k48i9xgsfcmrn6r"))))
-  (build-system ruby-build-system)
-  (propagated-inputs
-    `(("ruby-bio-logger" ,ruby-bio-logger)))
-  (arguments
-   `(#:tests? #f)) ;; no bundler
-  (synopsis
-    "Functions and tools for tranforming and changing tab delimited and comma separated table files - useful for Excel sheets and SQL/RDF output")
-  (description
-    "Functions and tools for tranforming and changing tab delimited and comma separated table files - useful for Excel sheets and SQL/RDF output")
-  (home-page
-    "http://github.com/pjotrp/bioruby-table")
-  (license license:expat)))
-
-
-(define-public bio-vcf ; guix maybe ready
-(package
-  (name "bio-vcf")
-  (version "0.9.2")
-  (source
-    (origin
-      (method url-fetch)
-      (uri (rubygems-uri "bio-vcf" version))
-      (sha256
-        (base32
-          "1007bn0w8l11q867lxsyqnk0vgvv12skvk9gyglv7g44knr5vh4j"))))
-  (build-system ruby-build-system)
-  (arguments
-   `(#:tests? #f)) ;; no bundler/cucumber
-  (synopsis
-    "Smart lazy multi-threaded parser for VCF format with useful filtering and output rewriting (JSON, RDF etc.)")
-  (description
-    "Smart lazy multi-threaded parser for VCF format with useful filtering and output rewriting (JSON, RDF etc.)")
-  (home-page
-    "http://github.com/pjotrp/bioruby-vcf")
-  (license license:expat)))
-
 (define-public ruby-faraday
 (package
   (name "ruby-faraday")