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-rw-r--r--gnu/build/activation.scm13
-rw-r--r--gnu/packages/bioinformatics.scm160
-rw-r--r--gnu/packages/emacs.scm6
-rw-r--r--gnu/packages/gstreamer.scm39
-rw-r--r--gnu/packages/man.scm6
-rw-r--r--gnu/services/base.scm2
-rw-r--r--gnu/system.scm18
7 files changed, 236 insertions, 8 deletions
diff --git a/gnu/build/activation.scm b/gnu/build/activation.scm
index 64c3410baf..0c60355a1c 100644
--- a/gnu/build/activation.scm
+++ b/gnu/build/activation.scm
@@ -30,6 +30,7 @@
activate-/bin/sh
activate-modprobe
activate-firmware
+ activate-ptrace-attach
activate-current-system))
;;; Commentary:
@@ -335,6 +336,18 @@ by itself, without having to resort to a \"user helper\"."
(lambda (port)
(display directory port))))
+(define (activate-ptrace-attach)
+ "Allow users to PTRACE_ATTACH their own processes.
+
+This works around a regression introduced in the default \"security\" policy
+found in Linux 3.4 onward that prevents users from attaching to their own
+processes--see Yama.txt in the Linux source tree for the rationale. This
+sounds like an unacceptable restriction for little or no security
+improvement."
+ (call-with-output-file "/proc/sys/kernel/yama/ptrace_scope"
+ (lambda (port)
+ (display 0 port))))
+
(define %current-system
;; The system that is current (a symlink.) This is not necessarily the same
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9813d07e9c..e143fb2c55 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -30,13 +30,17 @@
#:use-module (gnu packages base)
#:use-module (gnu packages compression)
#:use-module (gnu packages java)
+ #:use-module (gnu packages maths)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
#:use-module (gnu packages python)
+ #:use-module (gnu packages statistics)
+ #:use-module (gnu packages swig)
#:use-module (gnu packages tbb)
#:use-module (gnu packages vim)
+ #:use-module (gnu packages xml)
#:use-module (gnu packages zip))
(define-public bedops
@@ -507,6 +511,57 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from
Illumina, Roche 454, and the SOLiD platform.")
(license license:gpl3)))
+(define-public grit
+ (package
+ (name "grit")
+ (version "2.0.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/nboley/grit/archive/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:phases
+ (alist-cons-after
+ 'unpack 'generate-from-cython-sources
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; Delete these C files to force fresh generation from pyx sources.
+ (delete-file "grit/sparsify_support_fns.c")
+ (delete-file "grit/call_peaks_support_fns.c")
+ (substitute* "setup.py"
+ (("Cython.Setup") "Cython.Build")
+ ;; Add numpy include path to fix compilation
+ (("pyx\", \\]")
+ (string-append "pyx\", ], include_dirs = ['"
+ (assoc-ref inputs "python-numpy")
+ "/lib/python2.7/site-packages/numpy/core/include/"
+ "']"))) #t)
+ %standard-phases)))
+ (inputs
+ `(("python-scipy" ,python2-scipy)
+ ("python-numpy" ,python2-numpy)
+ ("python-pysam" ,python2-pysam)
+ ("python-networkx" ,python2-networkx)))
+ (native-inputs
+ `(("python-cython" ,python2-cython)
+ ("python-setuptools" ,python2-setuptools)))
+ (home-page "http://grit-bio.org")
+ (synopsis "Tool for integrative analysis of RNA-seq type assays")
+ (description
+ "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
+full length transcript models. When none of these data sources are available,
+GRIT can be run by providing a candidate set of TES or TSS sites. In
+addition, GRIT can merge in reference junctions and gene boundaries. GRIT can
+also be run in quantification mode, where it uses a provided GTF file and just
+estimates transcript expression.")
+ (license license:gpl3+)))
+
(define-public hisat
(package
(name "hisat")
@@ -1001,6 +1056,111 @@ sequences.")
;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
(license license:gpl3+)))
+(define-public shogun
+ (package
+ (name "shogun")
+ (version "4.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "ftp://shogun-toolbox.org/shogun/releases/"
+ (version-major+minor version)
+ "/sources/shogun-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb"))))
+ (build-system cmake-build-system)
+ (arguments
+ '(#:tests? #f ;no check target
+ #:phases
+ (alist-cons-after
+ 'unpack 'delete-broken-symlinks
+ (lambda _
+ (for-each delete-file '("applications/arts/data"
+ "applications/asp/data"
+ "applications/easysvm/data"
+ "applications/msplicer/data"
+ "applications/ocr/data"
+ "examples/documented/data"
+ "examples/documented/matlab_static"
+ "examples/documented/octave_static"
+ "examples/undocumented/data"
+ "examples/undocumented/matlab_static"
+ "examples/undocumented/octave_static"
+ "tests/integration/data"
+ "tests/integration/matlab_static"
+ "tests/integration/octave_static"
+ "tests/integration/python_modular/tests"))
+ #t)
+ (alist-cons-after
+ 'unpack 'change-R-target-path
+ (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* '("src/interfaces/r_modular/CMakeLists.txt"
+ "src/interfaces/r_static/CMakeLists.txt"
+ "examples/undocumented/r_modular/CMakeLists.txt")
+ (("\\$\\{R_COMPONENT_LIB_PATH\\}")
+ (string-append (assoc-ref outputs "out")
+ "/lib/R/library/")))
+ #t)
+ (alist-cons-after
+ 'unpack 'fix-octave-modules
+ (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* '("src/interfaces/octave_modular/CMakeLists.txt"
+ "src/interfaces/octave_static/CMakeLists.txt")
+ (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
+ "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave"))
+
+ ;; change target directory
+ (substitute* "src/interfaces/octave_modular/CMakeLists.txt"
+ (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
+ (string-append (assoc-ref outputs "out")
+ "/share/octave/packages")))
+ #t)
+ (alist-cons-before
+ 'build 'set-HOME
+ ;; $HOME needs to be set at some point during the build phase
+ (lambda _ (setenv "HOME" "/tmp") #t)
+ %standard-phases))))
+ #:configure-flags
+ (list "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
+ ;;"-DJavaModular=ON" ;requires unpackaged jblas
+ ;;"-DRubyModular=ON" ;requires unpackaged ruby-narray
+ ;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist
+ ;;"-DLuaModular=ON" ;fails because lua doesn't build pkgconfig file
+ "-DOctaveModular=ON"
+ "-DOctaveStatic=ON"
+ "-DPythonModular=ON"
+ "-DPythonStatic=ON"
+ "-DRModular=ON"
+ "-DRStatic=ON"
+ "-DCmdLineStatic=ON")))
+ (inputs
+ `(("python" ,python)
+ ("numpy" ,python-numpy)
+ ("r" ,r)
+ ("octave" ,octave)
+ ("swig" ,swig)
+ ("hdf5" ,hdf5)
+ ("atlas" ,atlas)
+ ("arpack" ,arpack-ng)
+ ("lapack" ,lapack)
+ ("glpk" ,glpk)
+ ("libxml2" ,libxml2)
+ ("lzo" ,lzo)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (home-page "http://shogun-toolbox.org/")
+ (synopsis "Machine learning toolbox")
+ (description
+ "The Shogun Machine learning toolbox provides a wide range of unified and
+efficient Machine Learning (ML) methods. The toolbox seamlessly allows to
+combine multiple data representations, algorithm classes, and general purpose
+tools. This enables both rapid prototyping of data pipelines and extensibility
+in terms of new algorithms.")
+ (license license:gpl3+)))
+
(define-public vcftools
(package
(name "vcftools")
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 73246ab3b9..5eb9c4b44a 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -1,7 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2014 Alex Kost <alezost@gmail.com>
;;;
;;; This file is part of GNU Guix.
@@ -57,14 +57,14 @@
(define-public emacs
(package
(name "emacs")
- (version "24.4")
+ (version "24.5")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/emacs/emacs-"
version ".tar.xz"))
(sha256
(base32
- "1zflm6ac34s6v166p58ilxrxbxjm0q2wfc25f8y0mjml1lbr3qs7"))))
+ "0kn3rzm91qiswi0cql89kbv6mqn27rwsyjfb8xmwy9m5s8fxfiyx"))))
(build-system glib-or-gtk-build-system)
(arguments
'(#:phases (alist-cons-before
diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm
index ad0cfccca9..9758806cc5 100644
--- a/gnu/packages/gstreamer.scm
+++ b/gnu/packages/gstreamer.scm
@@ -20,7 +20,7 @@
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages gstreamer)
- #:use-module ((guix licenses) #:select (lgpl2.0+ bsd-2 bsd-3))
+ #:use-module ((guix licenses) #:select (lgpl2.0+ bsd-2 bsd-3 gpl2+))
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix build-system gnu)
@@ -39,6 +39,7 @@
#:use-module (gnu packages xiph)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+ #:use-module (gnu packages yasm)
#:use-module (gnu packages xml))
(define-public orc
@@ -247,6 +248,42 @@ GStreamer multimedia library. This set contains those plug-ins which the
developers consider to have good quality code and correct functionality.")
(license lgpl2.0+)))
+(define-public gst-libav
+ (package
+ (name "gst-libav")
+ (version "1.4.5")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://gstreamer.freedesktop.org/src/" name "/"
+ name "-" version ".tar.xz"))
+ (sha256
+ (base32
+ "1g7vg9amh3cc3nmc415h6g2rqxqi4wgwqi08hxfbpwq48ri64p30"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (add-before configure patch-/bin/sh
+ (lambda _
+ (substitute* "gst-libs/ext/libav/configure"
+ (("#! /bin/sh")
+ (string-append "#! "(which "sh")))))))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)
+ ("python" ,python)
+ ("yasm" ,yasm)))
+ (inputs
+ `(("gst-plugins-base" ,gst-plugins-base)
+ ("orc" ,orc)
+ ("zlib" ,zlib)))
+ (home-page "http://gstreamer.freedesktop.org/")
+ (synopsis "Plugins for the GStreamer multimedia library")
+ (description
+ "This GStreamer plugin supports a large number of audio and video
+compression formats through the use of the libav library.")
+ (license gpl2+)))
+
(define-public gst-plugins-base-0.10
(package (inherit gst-plugins-base)
(version "0.10.36")
diff --git a/gnu/packages/man.scm b/gnu/packages/man.scm
index f5bd339100..a92c6dd132 100644
--- a/gnu/packages/man.scm
+++ b/gnu/packages/man.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2014 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014 David Thompson <dthompson2@worcester.edu>
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
;;;
@@ -119,7 +119,7 @@ the traditional flat-text whatis databases.")
(define-public man-pages
(package
(name "man-pages")
- (version "3.69")
+ (version "3.82")
(source (origin
(method url-fetch)
(uri (string-append
@@ -127,7 +127,7 @@ the traditional flat-text whatis databases.")
version ".tar.xz"))
(sha256
(base32
- "18zzmdzjihdnyg4vamk0jp6v6826vrsgal3kqqxvfq9bzyrh8xm2"))))
+ "1c8q618shf469nfp55qrwjv9630fgq5abfk946xya9hw1bfp6wjl"))))
(build-system gnu-build-system)
(arguments
'(#:phases (alist-delete 'configure %standard-phases)
diff --git a/gnu/services/base.scm b/gnu/services/base.scm
index cd1ba0b7b9..956fa7efa0 100644
--- a/gnu/services/base.scm
+++ b/gnu/services/base.scm
@@ -499,7 +499,7 @@ the ``message of the day''."
"Return a service that runs libc's name service cache daemon (nscd) with the
given @var{config}---an @code{<nscd-configuration>} object. Optionally,
@code{#:name-services} is a list of packages that provide name service switch
- (NSS) modules needed by nscd."
+ (NSS) modules needed by nscd. @xref{Name Service Switch}, for an example."
(mlet %store-monad ((nscd.conf (nscd.conf-file config)))
(return (service
(documentation "Run libc's name service cache daemon (nscd).")
diff --git a/gnu/system.scm b/gnu/system.scm
index ece61adb2b..6cf12df604 100644
--- a/gnu/system.scm
+++ b/gnu/system.scm
@@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -680,6 +681,9 @@ etc."
(activate-firmware
(string-append #$firmware "/lib/firmware"))
+ ;; Let users debug their own processes!
+ (activate-ptrace-attach)
+
;; Run the services' activation snippets.
;; TODO: Use 'load-compiled'.
(for-each primitive-load '#$actions)
@@ -695,6 +699,20 @@ we're running in the final root."
(dmd-conf (dmd-configuration-file services)))
(gexp->file "boot"
#~(begin
+ (use-modules (guix build utils))
+
+ ;; Clean out /tmp and /var/run.
+ ;;
+ ;; XXX This needs to happen before service activations, so
+ ;; it has to be here, but this also implicitly assumes
+ ;; that /tmp and /var/run are on the root partition.
+ (false-if-exception (delete-file-recursively "/tmp"))
+ (false-if-exception (delete-file-recursively "/var/run"))
+ (false-if-exception (mkdir "/tmp"))
+ (false-if-exception (chmod "/tmp" #o1777))
+ (false-if-exception (mkdir "/var/run"))
+ (false-if-exception (chmod "/var/run" #o755))
+
;; Activate the system.
;; TODO: Use 'load-compiled'.
(primitive-load #$activate)
generated by cgit v1.2.3 (git 2.45.0) at 2024-12-19 01:03:04 +0000