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

1 files changed, 164 insertions, 0 deletions

diff --git a/gn/packages/clBLAS.scm b/gn/packages/clBLAS.scm
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+;;; 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 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 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)))))
+    
+