Merge branch 'master' into core-updates

8 files changed, 135 insertions, 18 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0d8a6d518c..12c9175ed3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,6 +29,7 @@
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
+  #:use-module (gnu packages algebra)
   #:use-module (gnu packages base)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
@@ -87,7 +89,7 @@ BAM files.")
 (define-public bedops
   (package
     (name "bedops")
-    (version "2.4.5")
+    (version "2.4.14")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/bedops/bedops/archive/v"
@@ -95,7 +97,7 @@ BAM files.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0wmg6j0icimlrnsidaxrzf3hfgjvlkkcwvpdg7n4gg7hdv2m9ni5"))))
+                "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f
@@ -615,6 +617,56 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
 other types of unwanted sequence from high-throughput sequencing reads.")
     (license license:expat)))
 
+(define-public diamond
+  (package
+    (name "diamond")
+    (version "0.7.9")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/bbuchfink/diamond/archive/v"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15"))
+              (snippet '(begin
+                          (delete-file "bin/diamond")
+                          #t))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f  ;no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'enter-source-dir
+                    (lambda _
+                      (chdir "src")
+                      #t))
+         (delete 'configure)
+         (replace 'install
+                  (lambda* (#:key outputs #:allow-other-keys)
+                    (let ((bin (string-append (assoc-ref outputs "out")
+                                              "/bin")))
+                      (mkdir-p bin)
+                      (copy-file "../bin/diamond"
+                                 (string-append bin "/diamond"))
+                      #t))))))
+    (native-inputs
+     `(("bc" ,bc)))
+    (inputs
+     `(("boost" ,boost)
+       ("zlib" ,zlib)))
+    (home-page "https://github.com/bbuchfink/diamond")
+    (synopsis "Accelerated BLAST compatible local sequence aligner")
+    (description
+     "DIAMOND is a BLAST-compatible local aligner for mapping protein and
+translated DNA query sequences against a protein reference database (BLASTP
+and BLASTX alignment mode).  The speedup over BLAST is up to 20,000 on short
+reads at a typical sensitivity of 90-99% relative to BLAST depending on the
+data and settings.")
+    (license (license:non-copyleft "file://src/COPYING"
+                                   "See src/COPYING in the distribution."))))
+
 (define-public edirect
   (package
     (name "edirect")
@@ -1063,7 +1115,7 @@ sequencing tag position and orientation.")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "http://pypi.python.org/packages/source/m/misopy/misopy-"
+                    "https://pypi.python.org/packages/source/m/misopy/misopy-"
                     version ".tar.gz"))
               (sha256
                (base32
diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm
index 2be5ea351a..670fc64de8 100644
--- a/gnu/packages/ebook.scm
+++ b/gnu/packages/ebook.scm
@@ -60,7 +60,7 @@
 (define-public calibre
   (package
     (name "calibre")
-    (version "2.29.0")
+    (version "2.30.0")
     (source
       (origin
         (method url-fetch)
@@ -69,7 +69,7 @@
                             version ".tar.xz"))
         (sha256
           (base32
-           "1n3cfnjnghhhsgzcbcvbr0gh191lhl6az09q1s68jhlcc2lski6l"))
+           "1k2rpn06nfzqjy5k6fh8pwfj8vbhpn7rgkpkkpz5n2fqg3z8ph1j"))
         ;; Remove non-free or doubtful code, see
         ;; https://lists.gnu.org/archive/html/guix-devel/2015-02/msg00478.html
         (modules '((guix build utils)))
diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm
index c5b55f30a2..eeb97cdc85 100644
--- a/gnu/packages/freedesktop.scm
+++ b/gnu/packages/freedesktop.scm
@@ -38,7 +38,9 @@
   #:use-module (gnu packages docbook)
   #:use-module (gnu packages glib)                ;intltool
   #:use-module (gnu packages xdisorg)
-  #:use-module (gnu packages xorg))
+  #:use-module (gnu packages xorg)
+  #:use-module (gnu packages doxygen)
+  #:use-module (gnu packages libffi))
 
 (define-public xdg-utils
   (package
@@ -197,3 +199,36 @@ Python")
 
 (define-public python2-pyxdg
   (package-with-python2 python-pyxdg))
+
+(define-public wayland
+  (package
+    (name "wayland")
+    (version "1.8.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://wayland.freedesktop.org/releases/"
+                                  name "-" version ".tar.xz"))
+              (sha256
+               (base32
+                "1j3gfzn8i0xhk3j34mwb2srrscjxfyi279jhyq80mz943j6r6z7i"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("doxygen" ,doxygen)
+       ("pkg-config" ,pkg-config)
+       ("xmlto" ,xmlto)
+       ("xsltproc" ,libxslt)))
+    (inputs
+     `(("docbook-xml" ,docbook-xml)
+       ("docbook-xsl" ,docbook-xsl)
+       ("expat" ,expat)
+       ("libffi" ,libffi)
+       ("libxml2" ,libxml2))) ; for XML_CATALOG_FILES
+    (home-page "http://wayland.freedesktop.org/")
+    (synopsis "Display server protocol")
+    (description
+     "Wayland is a protocol for a compositor to talk to its clients as well as
+a C library implementation of that protocol.  The compositor can be a standalone
+display server running on Linux kernel modesetting and evdev input devices, an X
+application, or a wayland client itself.  The clients can be traditional
+applications, X servers (rootless or fullscreen) or other display servers.")
+    (license license:x11)))
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index a7483ba94a..ad4acb787e 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -582,3 +582,26 @@ with lossy compression and typically provides 3x smaller file sizes compared
 to PNG when lossy compression is acceptable for the red/green/blue color
 channels.")
     (license license:bsd-3)))
+
+(define-public libmng
+  (package
+    (name "libmng")
+    (version "2.0.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/libmng/"
+                                  name "-" version ".tar.xz"))
+              (sha256
+               (base32
+                "1lvxnpds0vcf0lil6ia2036ghqlbl740c4d2sz0q5g6l93fjyija"))))
+    (build-system gnu-build-system)
+    (propagated-inputs
+     ;; These are all in the 'Libs.private' field of libmng.pc.
+     `(("lcms" ,lcms)
+       ("libjpeg" ,libjpeg)
+       ("zlib" ,zlib)))
+    (home-page "http://www.libmng.com/")
+    (synopsis "Library for handling MNG files")
+    (description
+     "Libmng is the MNG (Multiple-image Network Graphics) reference library.")
+    (license license:bsd-3)))
diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 5baf24cac0..84841d017c 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -24,12 +24,12 @@
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages base)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages commencement)
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages texlive)
   #:use-module (gnu packages perl)
@@ -57,8 +57,9 @@
        ("pkg-config" ,pkg-config)))
     (inputs
      `(("libx11" ,libx11)
-       ("gcc:lib" ,gcc-final "lib") ; for libiberty, needed for objdump support
-       ("zlib" ,zlib)))             ; also needed for objdump support
+       ;; For libiberty, needed for objdump support.
+       ("gcc:lib" ,(canonical-package gcc-4.8) "lib")
+       ("zlib" ,zlib)))                       ;also needed for objdump support
     (arguments
      `(#:modules ((guix build gnu-build-system)
                   (guix build utils)
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 7f6ec56151..3da9df92cc 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -166,7 +166,7 @@ the Nix package manager.")
   ;;
   ;; Note: use a short commit id; when using the long one, the limit on socket
   ;; file names is exceeded while running the tests.
-  (let ((commit "a43b55f"))
+  (let ((commit "684bf7c"))
     (package (inherit guix-0.8.2)
       (version (string-append "0.8.2." commit))
       (source (origin
@@ -176,7 +176,7 @@ the Nix package manager.")
                       (commit commit)))
                 (sha256
                  (base32
-                  "1r0l8gfh5nxc1j0sqj8ywkg280k9qbj7zsk33z84rvl7l0nwnk88"))
+                  "0fq9ajj17kbb0f1p79al2vcqah9sl0imayhggcp31c3vq0ahya9g"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (arguments
        (substitute-keyword-arguments (package-arguments guix-0.8.2)
diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm
index 3bc3145e8d..1cf72e1586 100644
--- a/gnu/packages/qt.scm
+++ b/gnu/packages/qt.scm
@@ -29,6 +29,8 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages cups)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages gl)
@@ -93,7 +95,7 @@ X11 (yet).")
 (define-public qt
   (package
     (name "qt")
-    (version "5.4.1")
+    (version "5.4.2")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://download.qt-project.org/official_releases/qt/"
@@ -103,7 +105,7 @@ X11 (yet).")
                                  version ".tar.xz"))
              (sha256
               (base32
-               "0q6qzakq8xihw91xv310qi3vyylq7x2bzdkjgy8sqxii2lgbjzhv"))
+               "09gay5cimfdb0apy60v7z4r4zkl2vjysdppzihpla8dp2c30fvcc"))
              (patches (list (search-patch "qt5-conflicting-typedefs.patch")
                             (search-patch "qt5-runpath.patch")))
              (snippet
@@ -119,12 +121,14 @@ webrtc/tools/e2e_quality/audio/perf")))))
     (inputs
      `(("alsa-lib" ,alsa-lib)
        ("dbus" ,dbus)
+       ("cups" ,cups)
        ("expat" ,expat)
        ("fontconfig" ,fontconfig)
        ("freetype" ,freetype)
        ("glib" ,glib)
        ("icu4c" ,icu4c)
        ("libjpeg" ,libjpeg)
+       ("libmng" ,libmng)
        ("libpci" ,pciutils)
        ("libpng" ,libpng)
        ("libx11" ,libx11)
@@ -143,10 +147,12 @@ webrtc/tools/e2e_quality/audio/perf")))))
        ("mysql" ,mysql)
        ("nss" ,nss)
        ("openssl" ,openssl)
+       ("postgresql" ,postgresql)
        ("pulseaudio" ,pulseaudio)
        ("pcre" ,pcre)
        ("sqlite" ,sqlite)
        ("udev" ,eudev)
+       ("unixodbc" ,unixodbc)
        ("xcb-util" ,xcb-util)
        ("xcb-util-image" ,xcb-util-image)
        ("xcb-util-keysyms" ,xcb-util-keysyms)
@@ -221,7 +227,7 @@ developers using C++ or QML, a CSS & JavaScript like language.")
 
 (define-public qt-4
   (package (inherit qt)
-    (version "4.8.6")
+    (version "4.8.7")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://download.qt-project.org/official_releases/qt/"
@@ -231,7 +237,7 @@ developers using C++ or QML, a CSS & JavaScript like language.")
                                  version ".tar.gz"))
              (sha256
               (base32
-               "0b036iqgmbbv37dgwwfihw3mihjbnw3kb5kaisdy0qi8nn8xs54b"))
+               "183fca7n7439nlhxyg1z7aky0izgbyll3iwakw4gwivy16aj5272"))
              (patches (map search-patch
                            '("qt4-ldflags.patch" "qt4-tests.patch")))))
     (inputs `(,@(alist-delete "libjpeg" (package-inputs qt))
diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm
index 8e53debcb3..d7223bc0ba 100644
--- a/gnu/packages/samba.scm
+++ b/gnu/packages/samba.scm
@@ -168,14 +168,14 @@ Desktops into Active Directory environments using the winbind daemon.")
 (define-public talloc
   (package
     (name "talloc")
-    (version "2.1.0")
+    (version "2.1.2")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://www.samba.org/ftp/talloc/talloc-"
+              (uri (string-append "https://www.samba.org/ftp/talloc/talloc-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "13zh628hzlp2v9vj70knnfac2xbxqrdhgap30csq4zv4h8w3j087"))))
+                "13c365f7y8idjf2v1jxdjpkc3lxdmsxxfxjx1ymianm7zjiph393"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (alist-replace