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

1 files changed, 245 insertions, 20 deletions

diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm
index 7756a97..361f2f0 100644
--- a/gn/packages/arrayfire.scm
+++ b/gn/packages/arrayfire.scm
@@ -17,14 +17,17 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gn packages arrayfire)
-  #:use-module ((guix licenses))
+  #:use-module (guix packages)
+  #: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)
+  #:use-module (guix utils)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages autotools)
+  #:use-module (gnu packages bootstrap)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages cmake)
@@ -33,47 +36,59 @@
   #:use-module (gnu packages image)
   #:use-module (gnu packages video)
   #:use-module (gnu packages textutils)
+  ;; #:use-module (gnu packages fftw)
+  ;; #: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 ldc)
+  #:use-module (gnu packages wget)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages ruby)
   #:use-module (gnu packages xorg)
-  #:use-module (gnu packages version-control)  
+  #:use-module (gnu packages version-control)
+  #:use-module (gnu packages zip)  
   #:use-module (gnu packages linux))
 
 (define-public arrayfire
-(let ((commit "9ca1ea0"))
-  (package
+(package
     (name "arrayfire")
-    (version "3.3.1-hotfix")
+    (version "3.3.1")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-              (url "https://github.com/arrayfire/arrayfire.git")
-              (commit commit)))
-              (file-name (string-append name "-" commit))
+              (method url-fetch)
+              (uri (string-append "http://arrayfire.com/arrayfire_source/arrayfire-full-" version 
+                                  ".tar.bz2"))
+              (file-name (string-append name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "067y98a9s78vpz7xsg889xnwfaza7c5gdv97yg9cgrdl0iljvsgp"))))
+                "045adww6dqmyz6kkfmq7xawi5v9a894yp5j9pzn6j568gi48pyqc"))))
     (native-inputs `(("autoconf" ,autoconf)
         ("automake" ,automake)
-        ("cmake" ,cmake)
         ("gawk" ,gawk)
+        ("git" ,git)
         ("glew" ,glew)
         ("libtool" ,libtool)
         ("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)
+       ("ocl-icd" ,ocl-icd)
        ("enca" ,enca)
        ("eudev" ,eudev)
        ("glew" ,glew)
        ("glib" ,glib)
        ("lapack" ,lapack)
+       ("scalapack" ,scalapack)
        ("libcap" ,libcap)
        ("libjpeg" ,libjpeg)
        ("libltdl" ,libltdl)
@@ -82,21 +97,26 @@
        ("mesa-utils" ,mesa-utils)
        ("python" ,python-2)
        ("freeimage" ,freeimage)
+       ("freeglut" ,freeglut)
        ("fftw" ,fftw)
        ("fftwf" ,fftwf)
        ("fftw-openmpi" ,fftw-openmpi)
        ("glew" ,glew)
        ("glu" ,glu)
        ("openblas" ,openblas)
-       ("git" ,git)
+       ("wget" ,wget)
        ("cmake" ,cmake)))
     (build-system cmake-build-system)
     (arguments 
-     `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release" "-DBUILD_OPENCL=OFF" "-DBUILD_GRAPHICS=OFF") #:tests? #f))     
+     `(#: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? #t))     
     (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 gpl2 gpl2+ gpl3 gpl3+)))))
+    (license (list license:gpl2 
+                   license:gpl2+ 
+                   license:gpl3 
+                   license:gpl3+))))
 
 (define-public glfw
   (package
@@ -110,10 +130,12 @@
               (base32
                "08pixv8hd5xsccf7l8cqcijjqaq4k4da8qbp77wggal2fq445ika"))))
     (build-system cmake-build-system)
-    (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON") #:tests? #f))
+    (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON") 
+                 #:tests? #f))
     (native-inputs `(("autoconf" ,autoconf)
         ("automake" ,automake)
         ("cmake" ,cmake)
+        ("git" ,git)
         ("libtool" ,libtool)
         ("libpthread-stubs" ,libpthread-stubs)
         ("pkg-config" ,pkg-config)))
@@ -136,5 +158,208 @@
     (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))))
+    (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")
+   (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)))))
+    
+
+    
+