aboutsummaryrefslogtreecommitdiff
path: root/gn
diff options
context:
space:
mode:
authorPjotr Prins2016-03-19 13:26:16 +0000
committerPjotr Prins2016-03-19 13:26:16 +0000
commit911267d487a270c3792f1216baaff8c7cca4611a (patch)
tree62dbd5c1c5e729eaeeee81bbe3b2af1d29d0ae30 /gn
parent002fbd72657b07802627f76eff4280e03be86323 (diff)
parentdfe1f18aecbc1bb8317f021b78e4757e37bd1538 (diff)
downloadguix-bioinformatics-911267d487a270c3792f1216baaff8c7cca4611a.tar.gz
Merge branch 'master' of github.com:Brainiarc7/guix-bioinformatics into dennis
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/arrayfire.scm146
-rw-r--r--gn/packages/clBLAS.scm32
-rw-r--r--gn/packages/gtest.scm76
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))))