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-rw-r--r--gnu/packages/bioinformatics.scm58
-rw-r--r--gnu/packages/ebook.scm4
-rw-r--r--gnu/packages/freedesktop.scm37
-rw-r--r--gnu/packages/image.scm23
-rw-r--r--gnu/packages/ocaml.scm7
-rw-r--r--gnu/packages/package-management.scm4
-rw-r--r--gnu/packages/qt.scm14
-rw-r--r--gnu/packages/samba.scm6
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
generated by cgit v1.2.3 (git 2.45.0) at 2024-12-22 09:28:06 +0000