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

1 files changed, 239 insertions, 10 deletions

diff --git a/gn/packages/pocl.scm b/gn/packages/pocl.scm
index c5cb8cb..7d61526 100644
--- a/gn/packages/pocl.scm
+++ b/gn/packages/pocl.scm
@@ -20,14 +20,21 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix git-download)
   #:use-module (guix download)
+  #:use-module (guix utils)
+  #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
   #:use-module (guix packages)
+  #:use-module (gnu packages)
+  #:use-module (srfi srfi-1)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages boost)
+  #:use-module (gnu packages bootstrap)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages cmake)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages image)
   #:use-module (gnu packages video)
@@ -38,13 +45,18 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages web)
+  #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
   #:use-module (gnu packages xorg)
-  #:use-module (gnu packages version-control)  
+  #:use-module (gnu packages xml)
+  #:use-module (gnu packages version-control)
+  #:use-module (gnu packages ruby)
+  #:use-module (gnu packages gnupg)
+  #:use-module ((gnu packages zip) #:prefix gnuzip:)
   #:use-module (gnu packages linux))
 
 (define-public pocl
-(let ((commit "a6f377a"))
+(let ((commit "7aefc52"))
   (package
     (name "pocl")
     (version (string-append "v09rc-" commit ))
@@ -56,7 +68,7 @@
               (file-name (string-append name "-" commit))
               (sha256
                (base32
-                "0b1y8c2y0xx5sqfpkkvgmp02czgmq5immypgm4hhpmp512hcj38j"))))
+                "03wbcxkx1w5kx0crangsnah0xq218bhb99vglmn00wcjhhw80qim"))))
 (native-inputs `(("autoconf" ,autoconf)
                 ("automake" ,automake)
                 ("libtool" ,libtool)
@@ -65,8 +77,8 @@
 (inputs        `(("python" ,python-2)
                ("boost" ,boost)
                ("dbus" ,dbus)
-               ("clang" ,clang)
-               ("clang-runtime" ,clang-runtime)
+               ("clang" ,clang-3.7.1)
+               ("clang-runtime" ,clang-runtime-3.7.1)
                ("enca" ,enca)
                ("eudev" ,eudev)
                ("fftw-openmpi" ,fftw-openmpi)
@@ -76,19 +88,28 @@
                ("libjpeg" ,libjpeg)
                ("libltdl" ,libltdl)
                ("libtiff" ,libtiff)
-               ("llvm" ,llvm)
+               ("llvm" ,llvm-3.7.1)
+               ("ocl-icd" ,ocl-icd)
+               ("opencl-headers" ,opencl-headers)
                ("mesa-utils" ,mesa-utils)
                ("openmpi" ,openmpi)
+               ("perl" ,perl)
                ("randrproto" ,randrproto)
                ("libxrandr" ,libxrandr)
                ("xineramaproto" ,xineramaproto)
                ("libxinerama" ,libxinerama)
                ("libxcursor" ,libxcursor)
                ("fftw-openmpi" ,fftw-openmpi)))
-    (build-system cmake-build-system)
-    (arguments 
-     `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release" "-DBUILD_SHARED_LIBS=ON")
-       #:tests? #f))                
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags '("--enable-icd")
+     #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-before
+          'configure 'rewrite-usr-bin
+          (lambda _
+                   (zero? (system* "./autogen.sh")))))))                
     (synopsis "pocl: Portable Computing Language (pocl) aims to become a MIT-licensed
      open source implementation of the OpenCL standard which can be easily adapted for
      new targets and devices, both for homogeneous CPU and heterogenous GPUs/accelerators.")
@@ -97,3 +118,211 @@
      new targets and devices, both for homogeneous CPU and heterogenous GPUs/accelerators.")
     (home-page "http://portablecl.org/")
     (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" ,gnuzip: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))))
+    
+(define (clang-runtime-from-llvm llvm hash)
+  (package
+    (name "clang-runtime")
+    (version (package-version llvm-3.7.1))
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://llvm.org/releases/"
+                           version "/compiler-rt-" version ".src.tar.xz"))
+       (sha256 
+        (base32 
+        "10c1mz2q4bdq9bqfgr3dirc6hz1h3sq8573srd5q5lr7m7j6jiwx"))))
+    (build-system cmake-build-system)
+    (native-inputs (package-native-inputs llvm))
+    (inputs
+     `(("llvm" ,llvm)))
+    (arguments
+     `(;; Don't use '-g' during the build to save space.
+       #:build-type "Release"))
+
+    (home-page "http://compiler-rt.llvm.org")
+    (synopsis "Runtime library for Clang/LLVM")
+    (description
+     "The \"clang-runtime\" library provides the implementations of run-time
+functions for C and C++ programs.  It also provides header files that allow C
+and C++ source code to interface with the \"sanitization\" passes of the clang
+compiler.  In LLVM this library is called \"compiler-rt\".")
+    (license license:ncsa)
+
+    ;; <http://compiler-rt.llvm.org/> doesn't list MIPS as supported.
+    (supported-systems (delete "mips64el-linux" %supported-systems))))
+
+(define (clang-from-llvm llvm clang-runtime hash)
+  (package
+    (name "clang")
+    (version (package-version llvm-3.7.1))
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://llvm.org/releases/"
+                           version "/cfe-" version ".src.tar.xz"))
+       (sha256 
+        (base32 
+         "0x065d0w9b51xvdjxwfzjxng0gzpbx45fgiaxpap45ragi61dqjn"))
+       (patches (list (search-patch "clang-libc-search-path.patch")))))
+    ;; Using cmake allows us to treat llvm as an external library.  There
+    ;; doesn't seem to be any way to do this with clang's autotools-based
+    ;; build system.
+    (build-system cmake-build-system)
+    (native-inputs (package-native-inputs llvm))
+    (inputs
+     `(("libxml2" ,libxml2)
+       ("libstdc++-4.9", libstdc++-4.9)
+       ("python" ,python-2)
+       ("gcc-lib" ,gcc "lib")
+       ,@(package-inputs llvm)))
+    (propagated-inputs
+     `(("llvm" ,llvm)
+       ("clang-runtime" ,clang-runtime)))
+    (arguments
+     `(#:configure-flags
+       (list "-DCLANG_INCLUDE_TESTS=True"
+
+             ;; Find libgcc_s, crtbegin.o, and crtend.o.
+             (string-append "-DGCC_INSTALL_PREFIX="
+                            (assoc-ref %build-inputs "gcc-lib"))
+
+             ;; Use a sane default include directory.
+             (string-append "-DC_INCLUDE_DIRS="
+                            (assoc-ref %build-inputs "libc")
+                            "/include"))
+
+       ;; Don't use '-g' during the build to save space.
+       #:build-type "Release"
+
+       #:phases (modify-phases %standard-phases
+                  (add-after
+                   'unpack 'set-glibc-file-names
+                   (lambda* (#:key inputs #:allow-other-keys)
+                     (let ((libc (assoc-ref inputs "libc"))
+                           (compiler-rt (assoc-ref inputs "clang-runtime")))
+                       (substitute* "lib/Driver/Tools.cpp"
+                         ;; Patch the 'getLinuxDynamicLinker' function to that
+                         ;; it uses the right dynamic linker file name.
+                         (("/lib64/ld-linux-x86-64.so.2")
+                          (string-append libc
+                                         ,(glibc-dynamic-linker)))
+
+                         ;; Link to libclang_rt files from clang-runtime.
+                         (("TC\\.getDriver\\(\\)\\.ResourceDir")
+                          (string-append "\"" compiler-rt "\"")))
+
+                       ;; Same for libc's libdir, to allow crt1.o & co. to be
+                       ;; found.
+                       (substitute* "lib/Driver/ToolChains.cpp"
+                         (("@GLIBC_LIBDIR@")
+                          (string-append libc "/lib")))))))))
+
+    ;; Clang supports the same environment variables as GCC.
+    (native-search-paths
+     (list (search-path-specification
+            (variable "CPATH")
+            (files '("include")))
+           (search-path-specification
+            (variable "LIBRARY_PATH")
+            (files '("lib" "lib64")))))
+
+    (home-page "http://clang.llvm.org")
+    (synopsis "C language family frontend for LLVM")
+    (description
+     "Clang is a compiler front end for the C, C++, Objective-C and
+Objective-C++ programming languages.  It uses LLVM as its back end.  The Clang
+project includes the Clang front end, the Clang static analyzer, and several
+code analysis tools.")
+    (license license:ncsa)))
+         
+(define-public llvm-3.7.1
+  (package (inherit llvm)
+    (version "3.7.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://llvm.org/releases/"
+                           version "/llvm-" version ".src.tar.xz"))
+       (sha256
+        (base32
+         "1masakdp9g2dan1yrazg7md5am2vacbkb3nahb3dchpc1knr8xxy"))))))
+
+(define-public clang-runtime-3.7.1
+  (clang-runtime-from-llvm
+   llvm-3.7.1
+   "0dl1kbrhz96djsxqr61iw5h788s7ncfpfb7aayixky1bhdaydcx4"))
+
+(define-public clang-3.7.1
+  (clang-from-llvm llvm clang-runtime
+                   "12yv3jwdjcbkrx7zjm8wh4jrvb59v8fdw4mnmz3zc1jb00p9k07w"))
+
+
+
+    
+