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

3 files changed, 225 insertions, 29 deletions

diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm
index 21c1895..446669c 100644
--- a/gn/packages/arrayfire.scm
+++ b/gn/packages/arrayfire.scm
@@ -40,9 +40,11 @@
   ;; #:use-module (gnu packages fftw-openmpi) - in algebra
   ;; #:use-module (gnu packages fftwf)
   #: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 web)
   #:use-module (gnu packages wget)
   #:use-module (gnu packages python)
@@ -73,7 +75,10 @@
         ("pkg-config" ,pkg-config)))
     (inputs `(("boost" ,boost)
        ("glfw" ,glfw)
+       ("compute" ,compute)
        ("curl" ,curl)
+       ("clBLAS" ,clBLAS)
+       ("clFFT" ,clFFT)
        ("atlas" ,atlas)
        ("dbus" ,dbus)
        ("opencl-headers" ,opencl-headers)
@@ -103,10 +108,10 @@
        ("cmake" ,cmake)))
     (build-system cmake-build-system)
     (arguments 
-     `(#:configure-flags '("-DBUILD_OPENCL=OFF" "-DBUILD_CUDA=OFF" "-DBUILD_GRAPHICS=OFF") 
+     `(#:configure-flags '("-DBUILD_OPENCL=ON" "-DBUILD_CUDA=OFF" "-DBUILD_GRAPHICS=OFF" "-DUSE_SYSTEM_BOOST_COMPUTE=ON" "-DUSE_SYSTEM_CLBLAS=ON" "-DUSE_SYSTEM_CLFFT=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.")
+    (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.Now on Guix")
     (home-page "http://arrayfire.com/")
     (license (list license:gpl2 
                    license:gpl2+ 
@@ -155,6 +160,139 @@
     (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 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 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 compute
+  (package
+    (name "compute")
+    (version "v0.5")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append "https://github.com/boostorg/compute/archive/"
+                                 version ".tar.gz"))
+             (sha256
+              (base32
+               "1r16zd1wdnn9gx278mkvr13k3i79hr35v6vj0fn7v3n92ngwxnhd"))))
+    (build-system cmake-build-system)    
+    (arguments `(#:configure-flags '("-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)
+       ("boost" ,boost)
+       ("libcap" ,libcap)
+       ("libjpeg" ,libjpeg)
+       ("libltdl" ,libltdl)
+       ("libtiff" ,libtiff)
+       ("mesa-utils" ,mesa-utils)
+       ("openmpi" ,openmpi)
+       ("opencl-headers" ,opencl-headers)
+       ("ocl-icd" ,ocl-icd)
+       ("randrproto" ,randrproto)
+       ("libxrandr" ,libxrandr)
+       ("xineramaproto" ,xineramaproto)
+       ("libxinerama" ,libxinerama)
+       ("libxcursor" ,libxcursor)
+       ("python" ,python-2)))       
+    (home-page "http://boost.org")
+    (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")
@@ -220,4 +358,8 @@
     (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/clBLAS.scm b/gn/packages/clBLAS.scm
index 561ee2b..17a4589 100644
--- a/gn/packages/clBLAS.scm
+++ b/gn/packages/clBLAS.scm
@@ -61,7 +61,8 @@
               (base32
                "0adlb02lqzrklfybhnv4n0p37mvkvdi3vqiwa05x2mv05ywnr93j"))))
     (build-system cmake-build-system)    
-    (arguments `(#:configure-flags '("../clBLAS-2.10/src" "-DBUILD_SHARED_LIBS=ON" "-DCMAKE_BUILD_TYPE=Release") #:tests? #f))
+    (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)
@@ -70,11 +71,11 @@
         ("pkg-config" ,pkg-config)))
     (inputs `(("curl" ,curl)
        ("dbus" ,dbus)
+       ("boost" ,boost)
        ("enca" ,enca)
        ("eudev" ,eudev)
        ("fftw-openmpi" ,fftw-openmpi)
-       ("glew" ,glew)
-       ("googletest" ,googletest)
+       ("glew" ,glew)       
        ("libcap" ,libcap)
        ("libjpeg" ,libjpeg)
        ("libltdl" ,libltdl)
@@ -82,7 +83,6 @@
        ("mesa-utils" ,mesa-utils)
        ("openmpi" ,openmpi)
        ("ocl-icd" ,ocl-icd)
-       ("openblas" ,openblas)
        ("opencl-headers" ,opencl-headers)
        ("randrproto" ,randrproto)
        ("libxrandr" ,libxrandr)
@@ -161,26 +161,4 @@
     (home-page "https://www.khronos.org/registry/cl/")
     (license (list license:gpl2)))))
     
-(define-public googletest
-  (package
-    (name "googletest")
-    (version "1.7.0")
-    (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/google/googletest/archive/release-"
-                                 version ".tar.gz"))
-             (sha256
-              (base32
-               "1k0nf1l9cb3prdmsvaajl5i31bx86c1mw0d5jgzykz7rzm36afpp"))))
-    (build-system cmake-build-system)
-    (arguments `(#:configure-flags '("-DCMAKE_BUILD_TYPE=RelWithDebInfo") #:tests? #f))    
-    (inputs `(("automake" ,automake)
-       ("autoconf" ,autoconf)
-       ("libtool" ,libtool)
-       ("cmake" ,cmake)
-       ("python" ,python-2)
-       ("pkg-config" ,pkg-config)))       
-    (home-page "https://github.com/google/googletest")
-    (synopsis "Google's C++ test framework")
-    (description "Google's C++ test framework")
-    (license (list license:gpl2))))
+
diff --git a/gn/packages/gtest.scm b/gn/packages/gtest.scm
new file mode 100644
index 0000000..f8b34e9
--- /dev/null
+++ b/gn/packages/gtest.scm
@@ -0,0 +1,76 @@
+;;; 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 gtest)
+  #: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 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 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 zip)  
+  #:use-module (gnu packages linux))
+
+(define-public gtest 
+  (let ((revision "1")
+        (commit "13206d6f53aaff844f2d3595a01ac83a29e383db"))
+    (package
+      (name "gtest")
+      (version (string-append "1.7.0." revision "." commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url
+                "https://github.com/google/googletest.git")
+               (commit commit)))
+         (file-name (string-append name "-" version "-checkout"))
+         (sha256
+          (base32
+           "1v73r7wm9q9kpjbpbk0qs15703y2caaz6dkvz9bkn7nnv98jbqqc"))))
+      (build-system cmake-build-system)
+      (native-inputs
+       `(("python" ,python-wrapper)))
+      (synopsis "")
+      (description
+       "")
+      (home-page "")
+      (license license:expat))))