Merge branch 'master' into core-updates
Mark H Weaver
commit
412bee5e29
|
|
@ -240,8 +240,10 @@ SCM_TESTS = \
|
|||
tests/challenge.scm \
|
||||
tests/cve.scm \
|
||||
tests/file-systems.scm \
|
||||
tests/system.scm \
|
||||
tests/services.scm \
|
||||
tests/containers.scm
|
||||
tests/containers.scm \
|
||||
tests/import-utils.scm
|
||||
|
||||
if HAVE_GUILE_JSON
|
||||
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2012, 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -78,6 +78,9 @@
|
|||
(license . ,(package-license package))
|
||||
(home-page . ,(package-home-page package))
|
||||
(maintainers . ("bug-guix@gnu.org"))
|
||||
(max-silent-time . ,(or (assoc-ref (package-properties package)
|
||||
'max-silent-time)
|
||||
3600)) ; 1 hour by default
|
||||
(timeout . ,(or (assoc-ref (package-properties package) 'timeout)
|
||||
72000)))) ; 20 hours by default
|
||||
|
||||
|
|
|
|||
143
doc/guix.texi
143
doc/guix.texi
|
|
@ -399,6 +399,21 @@ for instance with:
|
|||
# ln -s /var/guix/profiles/per-user/root/guix-profile/bin/guix
|
||||
@end example
|
||||
|
||||
It is also a good idea to make the Info version of this manual available
|
||||
there:
|
||||
|
||||
@example
|
||||
# mkdir -p /usr/local/share/info
|
||||
# cd /usr/local/share/info
|
||||
# for i in /var/guix/profiles/per-user/root/guix-profile/share/info/* ;
|
||||
do ln -s $i ; done
|
||||
@end example
|
||||
|
||||
That way, assuming @file{/usr/local/share/info} is in the search path,
|
||||
running @command{info guix} will open this manual (@pxref{Other Info
|
||||
Directories,,, texinfo, GNU Texinfo}, for more details on changing the
|
||||
Info search path.)
|
||||
|
||||
@item
|
||||
To use substitutes from @code{hydra.gnu.org} (@pxref{Substitutes}),
|
||||
authorize them:
|
||||
|
|
@ -754,7 +769,7 @@ machines, since offloading works by invoking the @code{guix archive} and
|
|||
this is the case by running:
|
||||
|
||||
@example
|
||||
lsh build-machine guile -c '(use-modules (guix config))'
|
||||
lsh build-machine guile -c "'(use-modules (guix config))'"
|
||||
@end example
|
||||
|
||||
There's one last thing to do once @file{machines.scm} is in place. As
|
||||
|
|
@ -3973,6 +3988,14 @@ Keep the build tree of failed builds. Thus, if a build fail, its build
|
|||
tree is kept under @file{/tmp}, in a directory whose name is shown at
|
||||
the end of the build log. This is useful when debugging build issues.
|
||||
|
||||
@item --keep-going
|
||||
@itemx -k
|
||||
Keep going when some of the derivations fail to build; return only once
|
||||
all the builds have either completed or failed.
|
||||
|
||||
The default behavior is to stop as soon as one of the specified
|
||||
derivations has failed.
|
||||
|
||||
@item --dry-run
|
||||
@itemx -n
|
||||
Do not build the derivations.
|
||||
|
|
@ -4271,11 +4294,12 @@ guix import cpan Acme::Boolean
|
|||
|
||||
@item cran
|
||||
@cindex CRAN
|
||||
@cindex Bioconductor
|
||||
Import meta-data from @uref{http://cran.r-project.org/, CRAN}, the
|
||||
central repository for the @uref{http://r-project.org, GNU@tie{}R
|
||||
statistical and graphical environment}.
|
||||
|
||||
Information is extracted from the package's DESCRIPTION file.
|
||||
Information is extracted from the package's @code{DESCRIPTION} file.
|
||||
|
||||
The command command below imports meta-data for the @code{Cairo}
|
||||
R package:
|
||||
|
|
@ -4284,6 +4308,21 @@ R package:
|
|||
guix import cran Cairo
|
||||
@end example
|
||||
|
||||
When @code{--archive=bioconductor} is added, meta-data is imported from
|
||||
@uref{http://www.bioconductor.org/, Bioconductor}, a repository of R
|
||||
packages for for the analysis and comprehension of high-throughput
|
||||
genomic data in bioinformatics.
|
||||
|
||||
Information is extracted from a package's @code{DESCRIPTION} file
|
||||
published on the web interface of the Bioconductor SVN repository.
|
||||
|
||||
The command command below imports meta-data for the @code{GenomicRanges}
|
||||
R package:
|
||||
|
||||
@example
|
||||
guix import cran --archive=bioconductor GenomicRanges
|
||||
@end example
|
||||
|
||||
@item nix
|
||||
Import meta-data from a local copy of the source of the
|
||||
@uref{http://nixos.org/nixpkgs/, Nixpkgs distribution}@footnote{This
|
||||
|
|
@ -4482,6 +4521,8 @@ the updater for GNOME packages;
|
|||
the updater for @uref{http://elpa.gnu.org/, ELPA} packages;
|
||||
@item cran
|
||||
the updater for @uref{http://cran.r-project.org/, CRAN} packages;
|
||||
@item bioconductor
|
||||
the updater for @uref{http://www.bioconductor.org/, Bioconductor} R packages;
|
||||
@item pypi
|
||||
the updater for @uref{https://pypi.python.org, PyPI} packages.
|
||||
@end table
|
||||
|
|
@ -5674,17 +5715,23 @@ above, such as @code{host-name} and @code{bootloader}, are mandatory.
|
|||
Others, such as @code{packages} and @code{services}, can be omitted, in
|
||||
which case they get a default value.
|
||||
|
||||
Below we discuss the effect of some of the most important fields
|
||||
(@pxref{operating-system Reference}, for details about all the available
|
||||
fields), and how to @dfn{instantiate} the operating system using
|
||||
@command{guix system}.
|
||||
|
||||
@unnumberedsubsubsec Globally-Visible Packages
|
||||
|
||||
@vindex %base-packages
|
||||
The @code{packages} field lists
|
||||
packages that will be globally visible on the system, for all user
|
||||
accounts---i.e., in every user's @code{PATH} environment variable---in
|
||||
addition to the per-user profiles (@pxref{Invoking guix package}). The
|
||||
@var{%base-packages} variable provides all the tools one would expect
|
||||
for basic user and administrator tasks---including the GNU Core
|
||||
Utilities, the GNU Networking Utilities, the GNU Zile lightweight text
|
||||
editor, @command{find}, @command{grep}, etc. The example above adds
|
||||
tcpdump to those, taken from the @code{(gnu packages admin)} module
|
||||
(@pxref{Package Modules}).
|
||||
The @code{packages} field lists packages that will be globally visible
|
||||
on the system, for all user accounts---i.e., in every user's @code{PATH}
|
||||
environment variable---in addition to the per-user profiles
|
||||
(@pxref{Invoking guix package}). The @var{%base-packages} variable
|
||||
provides all the tools one would expect for basic user and administrator
|
||||
tasks---including the GNU Core Utilities, the GNU Networking Utilities,
|
||||
the GNU Zile lightweight text editor, @command{find}, @command{grep},
|
||||
etc. The example above adds tcpdump to those, taken from the @code{(gnu
|
||||
packages admin)} module (@pxref{Package Modules}).
|
||||
|
||||
@findex specification->package
|
||||
Referring to packages by variable name, like @var{tcpdump} above, has
|
||||
|
|
@ -5706,6 +5753,8 @@ version:
|
|||
%base-packages)))
|
||||
@end lisp
|
||||
|
||||
@unnumberedsubsubsec System Services
|
||||
|
||||
@vindex %base-services
|
||||
The @code{services} field lists @dfn{system services} to be made
|
||||
available when the system starts (@pxref{Services}).
|
||||
|
|
@ -5754,10 +5803,24 @@ more, would look like this:
|
|||
@xref{Desktop Services}, for the exact list of services provided by
|
||||
@var{%desktop-services}. @xref{X.509 Certificates}, for background
|
||||
information about the @code{nss-certs} package that is used here.
|
||||
@xref{operating-system Reference}, for details about all the available
|
||||
@code{operating-system} fields.
|
||||
|
||||
Assuming the above snippet is stored in the @file{my-system-config.scm}
|
||||
Again, @var{%desktop-services} is just a list of service objects. If
|
||||
you want to remove services from there, you can do so using the
|
||||
procedures for list filtering (@pxref{SRFI-1 Filtering and
|
||||
Partitioning,,, guile, GNU Guile Reference Manual}). For instance, the
|
||||
following expression returns a list that contains all the services in
|
||||
@var{%desktop-services} minus the Avahi service:
|
||||
|
||||
@example
|
||||
(remove (lambda (service)
|
||||
(eq? (service-kind service) avahi-service-type))
|
||||
%desktop-services)
|
||||
@end example
|
||||
|
||||
@unnumberedsubsubsec Instantiating the System
|
||||
|
||||
Assuming the @code{operating-system} declaration
|
||||
is stored in the @file{my-system-config.scm}
|
||||
file, the @command{guix system reconfigure my-system-config.scm} command
|
||||
instantiates that configuration, and makes it the default GRUB boot
|
||||
entry (@pxref{Invoking guix system}).
|
||||
|
|
@ -5779,6 +5842,8 @@ something went wrong with the latest generation. Reassuring, no? The
|
|||
@command{guix system list-generations} command lists the system
|
||||
generations available on disk.
|
||||
|
||||
@unnumberedsubsubsec The Programming Interface
|
||||
|
||||
At the Scheme level, the bulk of an @code{operating-system} declaration
|
||||
is instantiated with the following monadic procedure (@pxref{The Store
|
||||
Monad}):
|
||||
|
|
@ -5792,6 +5857,11 @@ the packages, configuration files, and other supporting files needed to
|
|||
instantiate @var{os}.
|
||||
@end deffn
|
||||
|
||||
This procedure is provided by the @code{(gnu system)} module. Along
|
||||
with @code{(gnu services)} (@pxref{Services}), this module contains the
|
||||
guts of GuixSD. Make sure to visit it!
|
||||
|
||||
|
||||
@node operating-system Reference
|
||||
@subsection @code{operating-system} Reference
|
||||
|
||||
|
|
@ -6288,7 +6358,7 @@ using the @code{locale} field of the @code{operating-system} declaration
|
|||
That locale must be among the @dfn{locale definitions} that are known to
|
||||
the system---and these are specified in the @code{locale-definitions}
|
||||
slot of @code{operating-system}. The default value includes locale
|
||||
definition for some widely used locales, but not for all the available
|
||||
definitions for some widely used locales, but not for all the available
|
||||
locales, in order to save space.
|
||||
|
||||
If the locale specified in the @code{locale} field is not among the
|
||||
|
|
@ -6762,13 +6832,14 @@ and lines for hidden services added via @code{tor-hidden-service}. Run
|
|||
@command{man tor} for information about the configuration file.
|
||||
@end deffn
|
||||
|
||||
@cindex hidden service
|
||||
@deffn {Scheme Procedure} tor-hidden-service @var{name} @var{mapping}
|
||||
Define a new Tor @dfn{hidden service} called @var{name} and implementing
|
||||
@var{mapping}. @var{mapping} is a list of port/host tuples, such as:
|
||||
|
||||
@example
|
||||
'((22 \"127.0.0.1:22\")
|
||||
(80 \"127.0.0.1:8080\"))
|
||||
'((22 "127.0.0.1:22")
|
||||
(80 "127.0.0.1:8080"))
|
||||
@end example
|
||||
|
||||
In this example, port 22 of the hidden service is mapped to local port 22, and
|
||||
|
|
@ -8907,7 +8978,7 @@ Now that you know all the features that initial RAM disks produced by
|
|||
further.
|
||||
|
||||
@deffn {Monadic Procedure} base-initrd @var{file-systems} @
|
||||
[#:qemu-networking? #f] [#:virtio? #f] [#:volatile-root? #f] @
|
||||
[#:qemu-networking? #f] [#:virtio? #t] [#:volatile-root? #f] @
|
||||
[#:extra-modules '()] [#:mapped-devices '()]
|
||||
Return a monadic derivation that builds a generic initrd. @var{file-systems} is
|
||||
a list of file-systems to be mounted by the initrd, possibly in addition to
|
||||
|
|
@ -10060,6 +10131,40 @@ If we also wanted GTK+ 3.8.2, this would be packaged as
|
|||
...))
|
||||
@end example
|
||||
|
||||
@c See <https://lists.gnu.org/archive/html/guix-devel/2016-01/msg00425.html>,
|
||||
@c for a discussion of what follows.
|
||||
@cindex version number, for VCS snapshots
|
||||
Occasionally, we package snapshots of upstream's version control system
|
||||
(VCS) instead of formal releases. This should remain exceptional,
|
||||
because it is up to upstream developers to clarify what the stable
|
||||
release is. Yet, it is sometimes necessary. So, what should we put in
|
||||
the @code{version} field?
|
||||
|
||||
Clearly, we need to make the commit identifier of the VCS snapshot
|
||||
visible in the version string, but we also need to make sure that the
|
||||
version string is monotonically increasing so that @command{guix package
|
||||
--upgrade} can determine which version is newer. Since commit
|
||||
identifiers, notably with Git, are not monotonically increasing, we add
|
||||
a revision number that we increase each time we upgrade to a newer
|
||||
snapshot. The resulting version string looks like this:
|
||||
|
||||
@example
|
||||
2.0.11-3.cabba9e
|
||||
^ ^ ^
|
||||
| | `-- upstream commit ID
|
||||
| |
|
||||
| `--- Guix package revision
|
||||
|
|
||||
latest upstream version
|
||||
@end example
|
||||
|
||||
It is a good idea to strip commit identifiers in the @code{version}
|
||||
field to, say, 7 digits. It avoids an aesthetic annoyance (assuming
|
||||
aesthetics have a role to play here) as well as problems related to OS
|
||||
limits such as the maximum shebang length (127 bytes for the Linux
|
||||
kernel.) It is best to use the full commit identifiers in
|
||||
@code{origin}s, though, to avoid ambiguities.
|
||||
|
||||
@node Synopses and Descriptions
|
||||
@subsection Synopses and Descriptions
|
||||
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
# GNU Guix --- Functional package management for GNU
|
||||
# Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
|
||||
# Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
|
||||
# Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
|
||||
# Copyright © 2013, 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
|
||||
#
|
||||
# This file is part of GNU Guix.
|
||||
|
|
@ -177,6 +177,7 @@ GNU_SYSTEM_MODULES = \
|
|||
gnu/packages/kodi.scm \
|
||||
gnu/packages/language.scm \
|
||||
gnu/packages/ldc.scm \
|
||||
gnu/packages/lego.scm \
|
||||
gnu/packages/less.scm \
|
||||
gnu/packages/lesstif.scm \
|
||||
gnu/packages/libcanberra.scm \
|
||||
|
|
@ -408,6 +409,7 @@ dist_patch_DATA = \
|
|||
gnu/packages/patches/agg-am_c_prototype.patch \
|
||||
gnu/packages/patches/alsa-lib-mips-atomic-fix.patch \
|
||||
gnu/packages/patches/apr-skip-getservbyname-test.patch \
|
||||
gnu/packages/patches/arb-ldconfig.patch \
|
||||
gnu/packages/patches/asymptote-gsl2.patch \
|
||||
gnu/packages/patches/ath9k-htc-firmware-binutils.patch \
|
||||
gnu/packages/patches/ath9k-htc-firmware-gcc.patch \
|
||||
|
|
@ -568,6 +570,7 @@ dist_patch_DATA = \
|
|||
gnu/packages/patches/libwmf-CVE-2015-4695.patch \
|
||||
gnu/packages/patches/libwmf-CVE-2015-4696.patch \
|
||||
gnu/packages/patches/libxslt-CVE-2015-7995.patch \
|
||||
gnu/packages/patches/linux-libre-CVE-2016-0728.patch \
|
||||
gnu/packages/patches/lirc-localstatedir.patch \
|
||||
gnu/packages/patches/libpthread-glibc-preparation.patch \
|
||||
gnu/packages/patches/lm-sensors-hwmon-attrs.patch \
|
||||
|
|
@ -686,6 +689,7 @@ dist_patch_DATA = \
|
|||
gnu/packages/patches/tidy-CVE-2015-5522+5523.patch \
|
||||
gnu/packages/patches/tinyxml-use-stl.patch \
|
||||
gnu/packages/patches/tk-find-library.patch \
|
||||
gnu/packages/patches/tophat-build-with-later-seqan.patch \
|
||||
gnu/packages/patches/torsocks-dns-test.patch \
|
||||
gnu/packages/patches/tvtime-gcc41.patch \
|
||||
gnu/packages/patches/tvtime-pngoutput.patch \
|
||||
|
|
|
|||
|
|
@ -41,7 +41,7 @@
|
|||
"Return #t if user namespaces can be created by unprivileged users."
|
||||
(let ((userns-file "/proc/sys/kernel/unprivileged_userns_clone"))
|
||||
(if (file-exists? userns-file)
|
||||
(string=? "1" (call-with-input-file userns-file read-string))
|
||||
(eqv? #\1 (call-with-input-file userns-file read-char))
|
||||
#t)))
|
||||
|
||||
(define (setgroups-supported?)
|
||||
|
|
|
|||
|
|
@ -6,6 +6,7 @@
|
|||
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
|
||||
;;; Copyright © 2015 Alex Sassmannshausen <alex.sassmannshausen@gmail.com>
|
||||
;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
|
||||
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -392,7 +393,7 @@ connection alive.")
|
|||
(bind-minor-version "9")
|
||||
(bind-patch-version "8")
|
||||
(bind-release-type "-P")
|
||||
(bind-release-version "2")
|
||||
(bind-release-version "3")
|
||||
(bind-version (string-append bind-major-version
|
||||
"."
|
||||
bind-minor-version
|
||||
|
|
@ -508,7 +509,7 @@ connection alive.")
|
|||
"/bind-" bind-version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0agkpmpna7s67la13krn4xlhwhdjpazmljxlq0zbjdwnw4k1k17m"))))
|
||||
"01qa17479jghy90lb2j8b1bpg3ay6k6aaajpigyirwzsvyc9yj3a"))))
|
||||
|
||||
;; When cross-compiling, we need the cross Coreutils and sed.
|
||||
;; Otherwise just use those from %FINAL-INPUTS.
|
||||
|
|
@ -1377,3 +1378,25 @@ command that learns\". It works by maintaining a database of the directories
|
|||
you use the most from the command line and allows you to \"jump\" to
|
||||
frequently used directories by typing only a small pattern.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public iftop
|
||||
(package
|
||||
(name "iftop")
|
||||
(version "1.0pre4")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "http://www.ex-parrot.com/~pdw/iftop/download"
|
||||
"/iftop-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"15sgkdyijb7vbxpxjavh5qm5nvyii3fqcg9mzvw7fx8s6zmfwczp"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
`(("libpcap" ,libpcap)
|
||||
("ncurses" ,ncurses)))
|
||||
(synopsis "Monitor network usage")
|
||||
(description "Iftop does for network usage what @command{top} does
|
||||
for CPU usage. It listens to network traffic on a named interface and
|
||||
displays a table of current bandwidth usage by pairs of hosts.")
|
||||
(home-page "http://www.ex-parrot.com/~pdw/iftop/")
|
||||
(license license:gpl3)))
|
||||
|
|
|
|||
|
|
@ -238,7 +238,7 @@ fast arithmetic.")
|
|||
(define-public arb
|
||||
(package
|
||||
(name "arb")
|
||||
(version "2.7.0")
|
||||
(version "2.8.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
|
|
@ -247,7 +247,8 @@ fast arithmetic.")
|
|||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1rwkffs57v8mry63rq8l2dyw69zfs9rg5fpbfllqp3nkjnkp1fly"))))
|
||||
"04hhcpshfkcq9fr4hixbhpps50yf9drk62xgkvlcaj5kb4nyrx7l"))
|
||||
(patches (map search-patch '("arb-ldconfig.patch")))))
|
||||
(build-system gnu-build-system)
|
||||
(propagated-inputs
|
||||
`(("flint" ,flint))) ; flint.h is included by arf.h
|
||||
|
|
|
|||
|
|
@ -3,7 +3,7 @@
|
|||
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
|
||||
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
|
||||
;;; Copyright © 2015 Alex Kost <alezost@gmail.com>
|
||||
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
|
||||
;;; Copyright © 2015, 2016 Mark H Weaver <mhw@netris.org>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -1535,14 +1535,14 @@ surround and reverb.")
|
|||
(define-public libxmp
|
||||
(package
|
||||
(name "libxmp")
|
||||
(version "4.3.8")
|
||||
(version "4.3.10")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "mirror://sourceforge/xmp/libxmp/"
|
||||
name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0h06091hlpgc6ds4pjmfq8sx4snw7av3nhny180q4pwfyasjb6ny"))))
|
||||
"1gm5xa0ca7ypcbj3bkmj3k1vvzl7nkch8gjyrm8p1a9vgzr0n761"))))
|
||||
(build-system gnu-build-system)
|
||||
(home-page "http://xmp.sourceforge.net/")
|
||||
(synopsis "Module player library")
|
||||
|
|
|
|||
|
|
@ -654,6 +654,73 @@ gapped, local, and paired-end alignment modes.")
|
|||
(supported-systems '("x86_64-linux"))
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public tophat
|
||||
(package
|
||||
(name "tophat")
|
||||
(version "2.1.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"http://ccb.jhu.edu/software/tophat/downloads/tophat-"
|
||||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7"))
|
||||
(patches (list (search-patch "tophat-build-with-later-seqan.patch")))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
'(begin
|
||||
;; Remove bundled SeqAn and samtools
|
||||
(delete-file-recursively "src/SeqAn-1.3")
|
||||
(delete-file-recursively "src/samtools-0.1.18")
|
||||
#t))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:parallel-build? #f ; not supported
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'use-system-samtools
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(substitute* "src/Makefile.in"
|
||||
(("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix)
|
||||
(("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "")
|
||||
(("SAMPROG = samtools_0\\.1\\.18") "")
|
||||
(("\\$\\(samtools_0_1_18_SOURCES\\)") "")
|
||||
(("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") ""))
|
||||
(substitute* '("src/common.cpp"
|
||||
"src/tophat.py")
|
||||
(("samtools_0.1.18") (which "samtools")))
|
||||
(substitute* '("src/common.h"
|
||||
"src/bam2fastx.cpp")
|
||||
(("#include \"bam.h\"") "#include <samtools/bam.h>")
|
||||
(("#include \"sam.h\"") "#include <samtools/sam.h>"))
|
||||
(substitute* '("src/bwt_map.h"
|
||||
"src/map2gtf.h"
|
||||
"src/align_status.h")
|
||||
(("#include <bam.h>") "#include <samtools/bam.h>")
|
||||
(("#include <sam.h>") "#include <samtools/sam.h>"))
|
||||
#t)))))
|
||||
(inputs
|
||||
`(("boost" ,boost)
|
||||
("bowtie" ,bowtie)
|
||||
("samtools" ,samtools-0.1)
|
||||
("ncurses" ,ncurses)
|
||||
("python" ,python-2)
|
||||
("perl" ,perl)
|
||||
("zlib" ,zlib)
|
||||
("seqan" ,seqan)))
|
||||
(home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
|
||||
(synopsis "Spliced read mapper for RNA-Seq data")
|
||||
(description
|
||||
"TopHat is a fast splice junction mapper for nucleotide sequence
|
||||
reads produced by the RNA-Seq method. It aligns RNA-Seq reads to
|
||||
mammalian-sized genomes using the ultra high-throughput short read
|
||||
aligner Bowtie, and then analyzes the mapping results to identify
|
||||
splice junctions between exons.")
|
||||
;; TopHat is released under the Boost Software License, Version 1.0
|
||||
;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
|
||||
(license license:boost1.0)))
|
||||
|
||||
(define-public bwa
|
||||
(package
|
||||
(name "bwa")
|
||||
|
|
@ -915,6 +982,64 @@ files between different genome assemblies. It supports most commonly used
|
|||
file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public cufflinks
|
||||
(package
|
||||
(name "cufflinks")
|
||||
(version "2.2.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "http://cole-trapnell-lab.github.io/"
|
||||
"cufflinks/assets/downloads/cufflinks-"
|
||||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1bnm10p8m7zq4qiipjhjqb24csiqdm1pwc8c795z253r2xk6ncg8"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:make-flags
|
||||
(list
|
||||
;; The includes for "eigen" are located in a subdirectory.
|
||||
(string-append "EIGEN_CPPFLAGS="
|
||||
"-I" (assoc-ref %build-inputs "eigen")
|
||||
"/include/eigen3/")
|
||||
;; Cufflinks must be linked with various boost libraries.
|
||||
(string-append "LDFLAGS="
|
||||
(string-join '("-lboost_system"
|
||||
"-lboost_serialization"
|
||||
"-lboost_thread"))))
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'fix-search-for-bam
|
||||
(lambda _
|
||||
(substitute* '("ax_bam.m4"
|
||||
"configure"
|
||||
"src/hits.h")
|
||||
(("<bam/sam\\.h>") "<samtools/sam.h>")
|
||||
(("<bam/bam\\.h>") "<samtools/bam.h>")
|
||||
(("<bam/version\\.hpp>") "<samtools/version.h>"))
|
||||
#t)))
|
||||
#:configure-flags
|
||||
(list (string-append "--with-bam="
|
||||
(assoc-ref %build-inputs "samtools")))))
|
||||
(inputs
|
||||
`(("eigen" ,eigen)
|
||||
("samtools" ,samtools-0.1)
|
||||
("htslib" ,htslib)
|
||||
("boost" ,boost)
|
||||
("python" ,python-2)
|
||||
("zlib" ,zlib)))
|
||||
(home-page "http://cole-trapnell-lab.github.io/cufflinks/")
|
||||
(synopsis "Transcriptome assembly and RNA-Seq expression analysis")
|
||||
(description
|
||||
"Cufflinks assembles RNA transcripts, estimates their abundances,
|
||||
and tests for differential expression and regulation in RNA-Seq
|
||||
samples. It accepts aligned RNA-Seq reads and assembles the
|
||||
alignments into a parsimonious set of transcripts. Cufflinks then
|
||||
estimates the relative abundances of these transcripts based on how
|
||||
many reads support each one, taking into account biases in library
|
||||
preparation protocols.")
|
||||
(license license:boost1.0)))
|
||||
|
||||
(define-public cutadapt
|
||||
(package
|
||||
(name "cutadapt")
|
||||
|
|
@ -3016,40 +3141,107 @@ optimized for modern read lengths of 100 bases or higher, and takes advantage
|
|||
of these reads to align data quickly through a hash-based indexing scheme.")
|
||||
(license license:asl2.0)))
|
||||
|
||||
(define-public sortmerna
|
||||
(package
|
||||
(name "sortmerna")
|
||||
(version "2.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"https://github.com/biocore/sortmerna/archive/"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1670a92x1vvkacnvgr2i5xac3ls6lp4pc3n0bccnmllsnymggcf0"))))
|
||||
(build-system gnu-build-system)
|
||||
(outputs '("out" ;for binaries
|
||||
"db")) ;for sequence databases
|
||||
(arguments
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let* ((out (assoc-ref outputs "out"))
|
||||
(bin (string-append out "/bin"))
|
||||
(db (assoc-ref outputs "db"))
|
||||
(share
|
||||
(string-append db "/share/sortmerna/rRNA_databases")))
|
||||
(install-file "sortmerna" bin)
|
||||
(install-file "indexdb_rna" bin)
|
||||
(for-each (lambda (file)
|
||||
(install-file file share))
|
||||
(find-files "rRNA_databases" ".*fasta"))
|
||||
#t))))))
|
||||
(home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
|
||||
(synopsis "Biological sequence analysis tool for NGS reads")
|
||||
(description
|
||||
"SortMeRNA is a biological sequence analysis tool for filtering, mapping
|
||||
and operational taxonomic unit (OTU) picking of next generation
|
||||
sequencing (NGS) reads. The core algorithm is based on approximate seeds and
|
||||
allows for fast and sensitive analyses of nucleotide sequences. The main
|
||||
application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
|
||||
(license license:lgpl3)))
|
||||
|
||||
(define-public star
|
||||
(package
|
||||
(name "star")
|
||||
(version "2.4.2a")
|
||||
(version "2.5.1b")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"https://github.com/alexdobin/STAR/archive/STAR_"
|
||||
(uri (string-append "https://github.com/alexdobin/STAR/archive/"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1c3rnm7r5l0kl3d04gl1g7938xqf1c2l0mla87rlplqg1hcns5mc"))
|
||||
"0wzcfhkg10apnh0y73xlarfa79xxwxdizicbdl11wb48awk44iq4"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
'(substitute* "source/Makefile"
|
||||
(("/bin/rm") "rm")))))
|
||||
'(begin
|
||||
(substitute* "source/Makefile"
|
||||
(("/bin/rm") "rm"))
|
||||
;; Remove pre-built binaries and bundled htslib sources.
|
||||
(delete-file-recursively "bin/MacOSX_x86_64")
|
||||
(delete-file-recursively "bin/Linux_x86_64")
|
||||
(delete-file-recursively "source/htslib")
|
||||
#t))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:tests? #f ;no check target
|
||||
#:make-flags '("STAR")
|
||||
#:phases
|
||||
(alist-cons-after
|
||||
'unpack 'enter-source-dir (lambda _ (chdir "source"))
|
||||
(alist-replace
|
||||
'install
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'enter-source-dir
|
||||
(lambda _ (chdir "source") #t))
|
||||
(add-after 'enter-source-dir 'do-not-use-bundled-htslib
|
||||
(lambda _
|
||||
(substitute* "Makefile"
|
||||
(("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib"
|
||||
_ prefix) prefix))
|
||||
(substitute* '("BAMfunctions.cpp"
|
||||
"signalFromBAM.h"
|
||||
"bam_cat.h"
|
||||
"bam_cat.c"
|
||||
"STAR.cpp"
|
||||
"bamRemoveDuplicates.cpp")
|
||||
(("#include \"htslib/([^\"]+\\.h)\"" _ header)
|
||||
(string-append "#include <" header ">")))
|
||||
(substitute* "IncludeDefine.h"
|
||||
(("\"htslib/(htslib/[^\"]+.h)\"" _ header)
|
||||
(string-append "<" header ">")))
|
||||
#t))
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
|
||||
(install-file "STAR" bin)))
|
||||
(alist-delete
|
||||
'configure %standard-phases)))))
|
||||
(install-file "STAR" bin))
|
||||
#t))
|
||||
(delete 'configure))))
|
||||
(native-inputs
|
||||
`(("vim" ,vim))) ; for xxd
|
||||
(inputs
|
||||
`(("zlib" ,zlib)))
|
||||
`(("htslib" ,htslib)
|
||||
("zlib" ,zlib)))
|
||||
(home-page "https://github.com/alexdobin/STAR")
|
||||
(synopsis "Universal RNA-seq aligner")
|
||||
(description
|
||||
|
|
@ -4002,7 +4194,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
|
|||
(define-public r-qtl
|
||||
(package
|
||||
(name "r-qtl")
|
||||
(version "1.37-11")
|
||||
(version "1.38-4")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
|
|
@ -4010,7 +4202,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
|
|||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0h20d36mww7ljp51pfs66xq33yq4b4fwq9nsh02dpmfhlaxgx1xi"))))
|
||||
"0rv9xhp8lyldpgwxqirhyjqvg07dr5x4x1x2jpyj37dada9ccyx3"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://rqtl.org/")
|
||||
(synopsis "R package for analyzing QTL experiments in genetics")
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com>
|
||||
;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -21,6 +22,7 @@
|
|||
#:use-module (guix packages)
|
||||
#:use-module (guix download)
|
||||
#:use-module (guix build-system gnu)
|
||||
#:use-module (guix build-system python)
|
||||
#:use-module (guix build-system glib-or-gtk)
|
||||
#:use-module ((guix licenses) #:prefix l:)
|
||||
#:use-module (gnu packages libevent)
|
||||
|
|
@ -33,6 +35,7 @@
|
|||
#:use-module (gnu packages gtk)
|
||||
#:use-module (gnu packages check)
|
||||
#:use-module (gnu packages ncurses)
|
||||
#:use-module (gnu packages python)
|
||||
#:use-module (gnu packages curl)
|
||||
#:use-module (gnu packages cyrus-sasl)
|
||||
#:use-module (gnu packages tls))
|
||||
|
|
@ -148,3 +151,44 @@ full encryption, DHT, PEX, and Magnet Links. It can also be controlled via
|
|||
XML-RPC over SCGI.")
|
||||
(home-page "https://github.com/rakshasa/rtorrent")
|
||||
(license l:gpl2+)))
|
||||
|
||||
(define-public transmission-remote-cli
|
||||
(package
|
||||
(name "transmission-remote-cli")
|
||||
(version "1.7.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/fagga/"
|
||||
"transmission-remote-cli/archive/v"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1y0hkpcjf6jw9xig8yf484hbhy63nip0pkchx401yxj81m25l4z9"))))
|
||||
(build-system python-build-system)
|
||||
(arguments
|
||||
`(#:python ,python-2 ; only supports Python 2
|
||||
#:tests? #f ; no test suite
|
||||
#:phases (modify-phases %standard-phases
|
||||
;; The software is just a Python script that must be
|
||||
;; copied into place.
|
||||
(delete 'build)
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let* ((out (assoc-ref outputs "out"))
|
||||
(bin (string-append out "/bin"))
|
||||
(man (string-append out "/share/man/man1"))
|
||||
;; FIXME install zsh completions
|
||||
(completions (string-append out "/etc/bash_completion.d")))
|
||||
(install-file "transmission-remote-cli" bin)
|
||||
(install-file "transmission-remote-cli.1" man)
|
||||
(install-file
|
||||
(string-append
|
||||
"completion/bash/"
|
||||
"transmission-remote-cli-bash-completion.sh")
|
||||
completions)))))))
|
||||
(synopsis "Console client for the Transmission BitTorrent daemon")
|
||||
(description "Transmission-remote-cli is a console client, with a curses
|
||||
interface, for the Transmission BitTorrent daemon.")
|
||||
(home-page "https://github.com/fagga/transmission-remote-cli")
|
||||
(license l:gpl3+)))
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org>
|
||||
;;; Copyright © 2014, 2015, 2016 Eric Bavier <bavier@member.fsf.org>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -169,7 +169,7 @@ tools that process C/C++ code.")
|
|||
(_ "UNSUPPORTED"))))
|
||||
(package
|
||||
(name "american-fuzzy-lop")
|
||||
(version "1.86b") ;It seems all releases have the 'b' suffix
|
||||
(version "1.96b") ;It seems all releases have the 'b' suffix
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
|
|
@ -177,7 +177,7 @@ tools that process C/C++ code.")
|
|||
"afl-" version ".tgz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1by9ncf6lgcyibzqwyla34jv64sd66mn8zhgjz2pcgsds51qwn0r"))))
|
||||
"0z7j231p6v2h1dxxijgdzj1lq1lxr8cxllwf6iyv7p4ki5pv1gh3"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
`(("custom-qemu"
|
||||
|
|
@ -190,11 +190,13 @@ tools that process C/C++ code.")
|
|||
;; afl only supports using a single afl-qemu-trace executable, so
|
||||
;; we only build qemu for the native target.
|
||||
(arguments
|
||||
`(#:configure-flags
|
||||
(list (string-append "--target-list=" ,machine "-linux-user"))
|
||||
#:modules ((srfi srfi-1)
|
||||
`(#:modules ((srfi srfi-1)
|
||||
,@%gnu-build-system-modules)
|
||||
,@(substitute-keyword-arguments (package-arguments qemu-2.3.0)
|
||||
((#:configure-flags config-flags)
|
||||
``(,(string-append "--target-list=" ,machine "-linux-user")
|
||||
,@(remove (λ (f) (string-prefix? "--target-list=" f))
|
||||
,config-flags)))
|
||||
((#:phases qemu-phases)
|
||||
`(modify-phases ,qemu-phases
|
||||
(add-after
|
||||
|
|
@ -236,7 +238,7 @@ tools that process C/C++ code.")
|
|||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||||
(let ((qemu (assoc-ref inputs "custom-qemu"))
|
||||
(out (assoc-ref outputs "out")))
|
||||
(copy-file (string-append qemu "/bin/qemu-" ,machine)
|
||||
(symlink (string-append qemu "/bin/qemu-" ,machine)
|
||||
(string-append out "/bin/afl-qemu-trace"))
|
||||
#t)))
|
||||
(delete 'check))))
|
||||
|
|
|
|||
|
|
@ -1,5 +1,7 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
|
||||
;;; Copyright © 2016 Mark H Weaver <mhw@netris.org>
|
||||
;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -63,14 +65,14 @@ and BOOTP/TFTP for network booting of diskless machines.")
|
|||
(define-public bind-utils
|
||||
(package
|
||||
(name "bind-utils")
|
||||
(version "9.10.3-P2")
|
||||
(version "9.10.3-P3")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "http://ftp.isc.org/isc/bind9/" version
|
||||
"/bind-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1kbfzml37sx4r2xi4gq48ji8w5kckd1f6gdn6pk6njqdmh8ijv2a"))))
|
||||
"10yblk8qbb85qxakzdjy5qmqvqj4rlcqsqvlkriglampzg8i0239"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
;; it would be nice to add GeoIP and gssapi once there is package
|
||||
|
|
@ -89,20 +91,24 @@ and BOOTP/TFTP for network booting of diskless machines.")
|
|||
(assoc-ref %build-inputs "mysql"))
|
||||
(string-append "--with-pkcs11="
|
||||
(assoc-ref %build-inputs "p11-kit")))
|
||||
#:modules ((srfi srfi-1)
|
||||
(srfi srfi-26)
|
||||
,@%gnu-build-system-modules)
|
||||
#:phases
|
||||
(alist-replace
|
||||
'build
|
||||
(let ((libs '("dns" "isc" "bind9" "isccfg" "lwres"))
|
||||
(bins '("dig" "nsupdate")))
|
||||
(modify-phases %standard-phases
|
||||
(replace 'build
|
||||
(lambda _
|
||||
(and (zero? (system* "make" "-C" "lib/dns"))
|
||||
(zero? (system* "make" "-C" "lib/isc"))
|
||||
(zero? (system* "make" "-C" "lib/bind9"))
|
||||
(zero? (system* "make" "-C" "lib/isccfg"))
|
||||
(zero? (system* "make" "-C" "lib/lwres"))
|
||||
(zero? (system* "make" "-C" "bin/dig"))))
|
||||
(alist-replace
|
||||
'install
|
||||
(lambda _ (zero? (system* "make" "-C" "bin/dig" "install")))
|
||||
%standard-phases))))
|
||||
(every (lambda (dir)
|
||||
(zero? (system* "make" "-C" dir)))
|
||||
(append (map (cut string-append "lib/" <>) libs)
|
||||
(map (cut string-append "bin/" <>) bins)))))
|
||||
(replace 'install
|
||||
(lambda _
|
||||
(every (lambda (dir)
|
||||
(zero? (system* "make" "-C" dir "install")))
|
||||
(map (cut string-append "bin/" <>) bins))))))))
|
||||
(home-page "https://www.isc.org/downloads/bind/")
|
||||
(synopsis "Tools for querying nameservers")
|
||||
(description
|
||||
|
|
|
|||
|
|
@ -60,7 +60,7 @@
|
|||
(define-public calibre
|
||||
(package
|
||||
(name "calibre")
|
||||
(version "2.48.0")
|
||||
(version "2.49.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
|
|
@ -69,7 +69,7 @@
|
|||
version ".tar.xz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0bjzw806czqxkhq9qqkhff8bhfc428pijkidb1h6gr47jqdp4hpg"))
|
||||
"0jc476pg07c0nwccprhwgjdlvvb2fdzza9xrjqzc0c42c5v7qzxa"))
|
||||
;; Remove non-free or doubtful code, see
|
||||
;; https://lists.gnu.org/archive/html/guix-devel/2015-02/msg00478.html
|
||||
(modules '((guix build utils)))
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2015 Tomáš Čech <sleep_walker@suse.cz>
|
||||
;;; Copyright © 2015 Daniel Pimentel <d4n1@member.fsf.org>
|
||||
;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -271,7 +271,7 @@ Libraries with some extra bells and whistles.")
|
|||
(define-public enlightenment
|
||||
(package
|
||||
(name "enlightenment")
|
||||
(version "0.20.2")
|
||||
(version "0.20.3")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri
|
||||
|
|
@ -279,7 +279,7 @@ Libraries with some extra bells and whistles.")
|
|||
name "/" name "-" version ".tar.xz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0faxky7lqd133jjjkr4c40kwwjhqc51ww10l3yy63671rfjhj424"))))
|
||||
"19z3bwdzwpzwi330l5g5mj7xy6wy8xrc39zivjhm0d1ql3fh649j"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:configure-flags '("--enable-mount-eeze")))
|
||||
|
|
|
|||
|
|
@ -32,7 +32,7 @@
|
|||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "http://jxself.org/" name ".tar.gz"))
|
||||
(uri (string-append "https://jxself.org/" name ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1hjcpy5439qs3v2zykis7hsi0i17zjs62gks3zd8mnfw9ni4i2h3"))))
|
||||
|
|
|
|||
|
|
@ -0,0 +1,67 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
||||
;;; under the terms of the GNU General Public License as published by
|
||||
;;; the Free Software Foundation; either version 3 of the License, or (at
|
||||
;;; your option) any later version.
|
||||
;;;
|
||||
;;; GNU Guix is distributed in the hope that it will be useful, but
|
||||
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
;;; GNU General Public License for more details.
|
||||
;;;
|
||||
;;; You should have received a copy of the GNU General Public License
|
||||
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
(define-module (gnu packages lego)
|
||||
#:use-module ((guix licenses) #:prefix license:)
|
||||
#:use-module (guix download)
|
||||
#:use-module (guix packages)
|
||||
#:use-module (guix build-system gnu)
|
||||
#:use-module (gnu packages)
|
||||
#:use-module (gnu packages bison)
|
||||
#:use-module (gnu packages flex))
|
||||
|
||||
(define-public nqc
|
||||
(package
|
||||
(name "nqc")
|
||||
(version "3.1.r6")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "http://bricxcc.sourceforge.net/nqc/release/"
|
||||
"nqc-" version ".tgz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0rp7pzr8xrdxpv75c2mi8zszzz2ypli4vvzxiic7mbrryrafdmdz"))))
|
||||
(build-system gnu-build-system)
|
||||
(native-inputs
|
||||
`(("bison" ,bison)
|
||||
("flex" ,flex)))
|
||||
(arguments
|
||||
'(#:tests? #f ;no tests
|
||||
#:make-flags (list (string-append "PREFIX=" %output))
|
||||
#:phases (modify-phases %standard-phases
|
||||
(delete 'configure)
|
||||
(add-before 'build 'rm-generated
|
||||
;; Regenerating compiler/lexer.cpp avoids an 'undefined
|
||||
;; reference to `isatty(int)'' error.
|
||||
(lambda _
|
||||
(for-each delete-file
|
||||
'("compiler/lexer.cpp"
|
||||
"compiler/parse.cpp"))
|
||||
#t))
|
||||
(add-after 'unpack 'deal-with-tarbomb
|
||||
(lambda _
|
||||
(chdir "..") ;tarbomb
|
||||
#t)))))
|
||||
(home-page "http://bricxcc.sourceforge.net/nqc/")
|
||||
(synopsis "C-like language for Lego's MINDSTORMS")
|
||||
(description
|
||||
"Not Quite C (NQC) is a simple language for programming several Lego
|
||||
MINDSTORMS products. The preprocessor and control structures of NQC are very
|
||||
similar to C. NQC is not a general purpose language -- there are many
|
||||
restrictions that stem from limitations of the standard RCX firmware.")
|
||||
(license license:mpl1.0)))
|
||||
|
|
@ -2,10 +2,10 @@
|
|||
;;; Copyright © 2012, 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
|
||||
;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org>
|
||||
;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
|
||||
;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
|
||||
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
|
||||
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
|
||||
;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
|
|
@ -286,7 +286,9 @@ for SYSTEM, or #f if there is no configuration for SYSTEM."
|
|||
(uri (linux-libre-urls version))
|
||||
(sha256
|
||||
(base32
|
||||
"1839xsaifs7vvyblzin8jps0gqi10xmz1l9p4x0j27vmdj39jgpm"))))
|
||||
"1839xsaifs7vvyblzin8jps0gqi10xmz1l9p4x0j27vmdj39jgpm"))
|
||||
(patches
|
||||
(list (search-patch "linux-libre-CVE-2016-0728.patch")))))
|
||||
(build-system gnu-build-system)
|
||||
(supported-systems '("x86_64-linux" "i686-linux"))
|
||||
(native-inputs `(("perl" ,perl)
|
||||
|
|
@ -1234,7 +1236,7 @@ processes currently causing I/O.")
|
|||
(define-public fuse
|
||||
(package
|
||||
(name "fuse")
|
||||
(version "2.9.4")
|
||||
(version "2.9.5")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (let ((version-with-underscores
|
||||
|
|
@ -1245,7 +1247,7 @@ processes currently causing I/O.")
|
|||
"/fuse-" version ".tar.gz")))
|
||||
(sha256
|
||||
(base32
|
||||
"1qbwp63a2bp0bchabkwiyzszi9x5krlk2pwk2is6g35gyszw1sbb"))))
|
||||
"1dfvbi1p57svbv2sfnbqwpnsk219spvjnlapf35azhgzqlf3g7sp"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs `(("util-linux" ,util-linux)))
|
||||
(arguments
|
||||
|
|
|
|||
|
|
@ -8,7 +8,8 @@
|
|||
;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
|
||||
;;; Copyright © 2015 Eric Bavier <bavier@member.fsf.org>
|
||||
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
|
||||
;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -519,7 +520,7 @@ MailCore 2.")
|
|||
(define-public claws-mail
|
||||
(package
|
||||
(name "claws-mail")
|
||||
(version "3.13.1")
|
||||
(version "3.13.2")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
|
|
@ -527,7 +528,7 @@ MailCore 2.")
|
|||
".tar.xz"))
|
||||
(sha256
|
||||
(base32
|
||||
"049av7r0xhjjjm1p93l2ns3xisvn125v3ncqar23cqjzgcichg5d"))))
|
||||
"1l8ankx0qpq1ix1an8viphcf11ksh53jsrm1xjmq8cjbh5910wva"))))
|
||||
(build-system gnu-build-system)
|
||||
(native-inputs `(("pkg-config" ,pkg-config)))
|
||||
(inputs `(("bogofilter" ,bogofilter)
|
||||
|
|
@ -1014,4 +1015,32 @@ compatibility shims for the @command{sendmail}, @command{mailq}, and
|
|||
@command{newaliases} commands.")
|
||||
(license gpl2+)))
|
||||
|
||||
(define-public fdm
|
||||
(package
|
||||
(name "fdm")
|
||||
(version "1.9")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/nicm/fdm/releases/download/"
|
||||
version "/fdm-"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32 "054rscijahiza5f9qha79rg3siji3bk5mk10f8c2vqx7m4w6qh8n"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
`(("tdb" ,tdb)
|
||||
("openssl" ,openssl)
|
||||
("zlib" ,zlib)))
|
||||
(home-page "https://github.com/nicm/fdm")
|
||||
(synopsis "Mail Retrieval Agent (MRA) and Mail Delivery Agent (MDA)")
|
||||
(description "fdm is a program designed to fetch mail from POP3
|
||||
or IMAP servers, or receive local mail from stdin, and
|
||||
deliver it in various ways.")
|
||||
(license
|
||||
;; Why point to a source file? Well, all the individual files have a
|
||||
;; copy of this license in their headers, but there's no seprate file
|
||||
;; with that information.
|
||||
(non-copyleft "https://github.com/nicm/fdm/blob/master/command.c"))))
|
||||
|
||||
;;; mail.scm ends here
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
|
||||
;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
|
||||
;;; Copyright © 2014 Julien Lepiller <julien@lepiller.eu>
|
||||
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
|
||||
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
|
||||
|
|
@ -425,7 +425,7 @@ was initially a fork of xmpppy, but is using non-blocking sockets.")
|
|||
(define-public gajim
|
||||
(package
|
||||
(name "gajim")
|
||||
(version "0.16.4")
|
||||
(version "0.16.5")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://gajim.org/downloads/"
|
||||
|
|
@ -433,10 +433,17 @@ was initially a fork of xmpppy, but is using non-blocking sockets.")
|
|||
"/gajim-" version ".tar.bz2"))
|
||||
(sha256
|
||||
(base32
|
||||
"0zyfs7q1qg8iqszr8l1gb18gqla6zrrfsgpmbxblpi9maqxas5i1"))))
|
||||
"14fhcqnkqygh91132dnf1idayj4r3iqbwb44sd3mxv20n6ribh55"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
`(;; The only check done by gajim-0.16.x is to check that the
|
||||
;; translations are up-to-date, and in 0.16.5 they are not, so
|
||||
;; "make check" fails. Therefore, we disable tests for now.
|
||||
;;
|
||||
;; XXX TODO Try re-enabling tests in gajim-0.16.6 or later.
|
||||
;;
|
||||
#:tests? #f
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'install 'wrap-program
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
|
||||
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
|
|
@ -328,7 +328,11 @@ you to define complex tempo maps for entire songs or performances.")
|
|||
music. Music is input in a text file containing control sequences which are
|
||||
interpreted by LilyPond to produce the final document. It is extendable with
|
||||
Guile.")
|
||||
(license license:gpl3+)))
|
||||
(license license:gpl3+)
|
||||
|
||||
;; On armhf and mips64el, building the documentation sometimes leads to
|
||||
;; more than an hour of silence, so double the max silent time.
|
||||
(properties `((max-silent-time . 7200)))))
|
||||
|
||||
(define-public non-sequencer
|
||||
;; The latest tagged release is three years old and uses a custom build
|
||||
|
|
@ -957,7 +961,7 @@ capabilities, custom envelopes, effects, etc.")
|
|||
(define-public yoshimi
|
||||
(package
|
||||
(name "yoshimi")
|
||||
(version "1.3.7.1")
|
||||
(version "1.3.8.2")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "mirror://sourceforge/yoshimi/"
|
||||
|
|
@ -965,7 +969,7 @@ capabilities, custom envelopes, effects, etc.")
|
|||
"/yoshimi-" version ".tar.bz2"))
|
||||
(sha256
|
||||
(base32
|
||||
"13xc1x8jrr2rn26jx4dini692ww3771d5j5xf7f56ixqr7mmdhvz"))))
|
||||
"0wl4ln6v1nkkx56kfah23chyrhga2vi93i82g0s200c4s4184xr8"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; there are no tests
|
||||
|
|
@ -1036,3 +1040,41 @@ graphically in the terminal. It is built on a full-featured subtractive
|
|||
synthesis engine. Notes and parameter changes may be entered via MIDI or the
|
||||
computer's keyboard.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public qtractor
|
||||
(package
|
||||
(name "qtractor")
|
||||
(version "0.7.3")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "http://downloads.sourceforge.net/qtractor/"
|
||||
"qtractor-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1vy4297myyqk0k58nzybgvgklckhngpdcnmp98k0rq98dirclbl7"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments `(#:tests? #f)) ; no "check" target
|
||||
(inputs
|
||||
`(("qt" ,qt)
|
||||
("alsa-lib" ,alsa-lib)
|
||||
("jack" ,jack-1)
|
||||
("libsndfile" ,libsndfile)
|
||||
("ladspa" ,ladspa)
|
||||
("lv2" ,lv2)
|
||||
("lilv" ,lilv)
|
||||
("suil" ,suil)
|
||||
("libsamplerate" ,libsamplerate)
|
||||
("libvorbis" ,libvorbis)
|
||||
("libmad" ,libmad)
|
||||
("rubberband" ,rubberband)
|
||||
("liblo" ,liblo)
|
||||
("zlib" ,zlib)))
|
||||
(native-inputs
|
||||
`(("pkg-config" ,pkg-config)))
|
||||
(home-page "http://qtractor.sourceforge.net/")
|
||||
(synopsis "Audio/MIDI multi-track sequencer")
|
||||
(description
|
||||
"Qtractor is an Audio/MIDI multi-track sequencer application. It uses
|
||||
JACK for audio and ALSA sequencer for MIDI as multimedia infrastructures and
|
||||
follows a traditional multi-track tape recorder control paradigm.")
|
||||
(license license:gpl2+)))
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org>
|
||||
;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -28,7 +28,7 @@
|
|||
(define-public nano
|
||||
(package
|
||||
(name "nano")
|
||||
(version "2.5.0")
|
||||
(version "2.5.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
|
|
@ -36,7 +36,7 @@
|
|||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1vl9bim56k1b4zwc3icxp46w6pn6gb042j1h4jlz1jklxxpkwcpz"))))
|
||||
"1piv8prj6w3rvsrrx41ra8c10b8fzkgjhnm6399lsgqqpw0wlvz0"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
`(("gettext" ,gnu-gettext)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,22 @@
|
|||
diff -u -r arb-2.8.1.orig/configure arb-2.8.1/configure
|
||||
--- arb-2.8.1.orig/configure 2015-12-31 17:30:01.000000000 +0100
|
||||
+++ arb-2.8.1/configure 2016-01-20 16:41:41.336726596 +0100
|
||||
@@ -647,6 +647,7 @@
|
||||
echo "ARB_SHARED=$SHARED" >> Makefile
|
||||
echo "ARB_LIB=$ARB_LIB" >> Makefile
|
||||
echo "ARB_LIBNAME=$ARB_LIBNAME" >> Makefile
|
||||
+echo "ARB_MAJOR=$ARB_MAJOR" >> Makefile
|
||||
echo "ARB_SOLIB=$ARB_SOLIB" >> Makefile
|
||||
echo "EXEEXT=$EXEEXT" >> Makefile
|
||||
echo "PREFIX=$PREFIX" >> Makefile
|
||||
diff -u -r arb-2.8.1.orig/Makefile.in arb-2.8.1/Makefile.in
|
||||
--- arb-2.8.1.orig/Makefile.in 2015-12-31 17:30:01.000000000 +0100
|
||||
+++ arb-2.8.1/Makefile.in 2016-01-20 16:30:32.575298517 +0100
|
||||
@@ -101,6 +101,7 @@
|
||||
$(LDCONFIG) -n "$(CURDIR)"; \
|
||||
fi
|
||||
ln -sf "$(ARB_LIB)" "$(ARB_LIBNAME)"; \
|
||||
+ ln -sf "$(ARB_LIB)" "$(ARB_LIBNAME).$(ARB_MAJOR)"; \
|
||||
|
||||
libarb.a: $(OBJS) $(LIB_SOURCES) $(EXT_SOURCES) $(HEADERS) $(EXT_HEADERS) | build build/interfaces
|
||||
$(AT)$(foreach ext, $(EXTENSIONS), $(foreach dir, $(patsubst $(ext)/%.h, %, $(wildcard $(ext)/*.h)), mkdir -p build/$(dir); BUILD_DIR=$(CURDIR)/build/$(dir); export BUILD_DIR; MOD_DIR=$(dir); export MOD_DIR; $(MAKE) -f $(CURDIR)/Makefile.subdirs -C $(ext)/$(dir) static || exit $$?;))
|
||||
|
|
@ -0,0 +1,84 @@
|
|||
Copied from
|
||||
https://git.kernel.org/cgit/linux/kernel/git/torvalds/linux.git/patch/?id=23567fd052a9abb6d67fe8e7a9ccdd9800a540f2
|
||||
|
||||
From 23567fd052a9abb6d67fe8e7a9ccdd9800a540f2 Mon Sep 17 00:00:00 2001
|
||||
From: Yevgeny Pats <yevgeny@perception-point.io>
|
||||
Date: Tue, 19 Jan 2016 22:09:04 +0000
|
||||
Subject: KEYS: Fix keyring ref leak in join_session_keyring()
|
||||
|
||||
This fixes CVE-2016-0728.
|
||||
|
||||
If a thread is asked to join as a session keyring the keyring that's already
|
||||
set as its session, we leak a keyring reference.
|
||||
|
||||
This can be tested with the following program:
|
||||
|
||||
#include <stddef.h>
|
||||
#include <stdio.h>
|
||||
#include <sys/types.h>
|
||||
#include <keyutils.h>
|
||||
|
||||
int main(int argc, const char *argv[])
|
||||
{
|
||||
int i = 0;
|
||||
key_serial_t serial;
|
||||
|
||||
serial = keyctl(KEYCTL_JOIN_SESSION_KEYRING,
|
||||
"leaked-keyring");
|
||||
if (serial < 0) {
|
||||
perror("keyctl");
|
||||
return -1;
|
||||
}
|
||||
|
||||
if (keyctl(KEYCTL_SETPERM, serial,
|
||||
KEY_POS_ALL | KEY_USR_ALL) < 0) {
|
||||
perror("keyctl");
|
||||
return -1;
|
||||
}
|
||||
|
||||
for (i = 0; i < 100; i++) {
|
||||
serial = keyctl(KEYCTL_JOIN_SESSION_KEYRING,
|
||||
"leaked-keyring");
|
||||
if (serial < 0) {
|
||||
perror("keyctl");
|
||||
return -1;
|
||||
}
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
If, after the program has run, there something like the following line in
|
||||
/proc/keys:
|
||||
|
||||
3f3d898f I--Q--- 100 perm 3f3f0000 0 0 keyring leaked-keyring: empty
|
||||
|
||||
with a usage count of 100 * the number of times the program has been run,
|
||||
then the kernel is malfunctioning. If leaked-keyring has zero usages or
|
||||
has been garbage collected, then the problem is fixed.
|
||||
|
||||
Reported-by: Yevgeny Pats <yevgeny@perception-point.io>
|
||||
Signed-off-by: David Howells <dhowells@redhat.com>
|
||||
Acked-by: Don Zickus <dzickus@redhat.com>
|
||||
Acked-by: Prarit Bhargava <prarit@redhat.com>
|
||||
Acked-by: Jarod Wilson <jarod@redhat.com>
|
||||
Signed-off-by: James Morris <james.l.morris@oracle.com>
|
||||
---
|
||||
security/keys/process_keys.c | 1 +
|
||||
1 file changed, 1 insertion(+)
|
||||
|
||||
diff --git a/security/keys/process_keys.c b/security/keys/process_keys.c
|
||||
index a3f85d2..e6d50172 100644
|
||||
--- a/security/keys/process_keys.c
|
||||
+++ b/security/keys/process_keys.c
|
||||
@@ -794,6 +794,7 @@ long join_session_keyring(const char *name)
|
||||
ret = PTR_ERR(keyring);
|
||||
goto error2;
|
||||
} else if (keyring == new->session_keyring) {
|
||||
+ key_put(keyring);
|
||||
ret = 0;
|
||||
goto error2;
|
||||
}
|
||||
--
|
||||
cgit v0.12
|
||||
|
||||
|
|
@ -0,0 +1,24 @@
|
|||
This patch resolves a build failure when building TopHat 2.1.0 with SeqAn 1.4.
|
||||
This is the relevant part of a patch originally posted here:
|
||||
https://lists.fu-berlin.de/pipermail/seqan-dev/2014-July/msg00001.html
|
||||
|
||||
--- a/src/segment_juncs.cpp
|
||||
+++ b/src/segment_juncs.cpp
|
||||
@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl
|
||||
typedef map<uint32_t, IntronMotifs> MotifMap;
|
||||
|
||||
MotifMap ims;
|
||||
-
|
||||
- seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
|
||||
- seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
|
||||
-
|
||||
+
|
||||
+ typedef seqan::ModifiedString<
|
||||
+ seqan::ModifiedString<seqan::DnaString const, seqan::ModView<seqan::FunctorComplement<seqan::Dna> > >,
|
||||
+ seqan::ModReverse> ConstDnaStringReverseComplement;
|
||||
+ ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
|
||||
+ ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
|
||||
+
|
||||
if (talkative)
|
||||
fprintf(stderr, "Collecting potential splice sites in islands\n");
|
||||
|
||||
|
|
@ -339,13 +339,13 @@ security, and applying best practice development processes.")
|
|||
(define-public acme
|
||||
(package
|
||||
(name "acme")
|
||||
(version "0.1.1")
|
||||
(version "0.2.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri "acme" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1yv0gy8akaqp5p2wjpfj8r5i0da04a9qdmlh06rczdkrmk6q680w"))))
|
||||
"1xcbywzrwrj2cmqhaj4k6b11wfkbm3i7za2k9j1sd74rs1zh5abl"))))
|
||||
(build-system python-build-system)
|
||||
(arguments
|
||||
`(#:python ,python-2))
|
||||
|
|
@ -371,13 +371,13 @@ security, and applying best practice development processes.")
|
|||
(define-public letsencrypt
|
||||
(package
|
||||
(name "letsencrypt")
|
||||
(version "0.1.1")
|
||||
(version "0.2.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri "letsencrypt" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1kia3wk66lxyi2fghp9sd7cqgr5qiwdfayz153hi4wpa3q1q8rwf"))))
|
||||
"0q57ylx00b6kl9zvawgag5yl03vlv1cjhp18xm96682pdibbgjci"))))
|
||||
(build-system python-build-system)
|
||||
(arguments
|
||||
`(#:python ,python-2))
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
|
||||
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -36,14 +37,14 @@
|
|||
(define-public tor
|
||||
(package
|
||||
(name "tor")
|
||||
(version "0.2.7.5")
|
||||
(version "0.2.7.6")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://www.torproject.org/dist/tor-"
|
||||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0pxayvcab4cb107ynbpzx4g0qyr1mjfba2an76wdx6dxn56rwakx"))))
|
||||
"0p8hjlfi8dwghlyjif5s0q98cmpgz9kn9jja25430l04z5wqcfj9"))))
|
||||
(build-system gnu-build-system)
|
||||
(native-inputs
|
||||
`(("python" ,python-2))) ; for tests
|
||||
|
|
@ -103,7 +104,7 @@ rejects UDP traffic from the application you're using.")
|
|||
(define-public privoxy
|
||||
(package
|
||||
(name "privoxy")
|
||||
(version "3.0.21")
|
||||
(version "3.0.24")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "mirror://sourceforge/ijbswa/Sources/"
|
||||
|
|
@ -111,7 +112,7 @@ rejects UDP traffic from the application you're using.")
|
|||
version "-stable-src.tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1f6xb7aa47p90c26vqaw74y6drs9gpnhxsgby3mx0awdjh0ydisy"))))
|
||||
"04mhkz5g713i2crvjd6s783hhrlsjjjlfb9llbaf13ghg3fgd0d3"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(;; The default 'sysconfdir' is $out/etc; change that to
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@
|
|||
;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
|
||||
;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
|
||||
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
|
||||
;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2015 Kyle Meyer <kyle@kyleam.com>
|
||||
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;;
|
||||
|
|
@ -1004,7 +1004,7 @@ modification time.")
|
|||
(define-public myrepos
|
||||
(package
|
||||
(name "myrepos")
|
||||
(version "1.20151022")
|
||||
(version "1.20160123")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
|
|
@ -1013,7 +1013,7 @@ modification time.")
|
|||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32 "0c93lqsngpsxsca7nygk4qhidr40ijgih86q81x1mfcwbs0gbds8"))))
|
||||
(base32 "1723cg5haplz2w9dwdzp6ds1ip33cx3awmj4wnb0h4yq171v5lqk"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
`(("perl" ,perl)))
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
|
||||
;;; Copyright © 2014, 2015 David Thompson <davet@gnu.org>
|
||||
;;; Copyright © 2014, 2015, 2016 David Thompson <davet@gnu.org>
|
||||
;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
|
||||
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
|
||||
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
|
||||
|
|
@ -1265,6 +1265,39 @@ functionality of the system is provided via an assortment of ready to use
|
|||
tools, XML authoring components, and an extensible plug-in based API.")
|
||||
(license license:lgpl2.1+)))
|
||||
|
||||
(define-public v4l-utils
|
||||
(package
|
||||
(name "v4l-utils")
|
||||
(version "1.8.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "http://linuxtv.org/downloads/v4l-utils"
|
||||
"/v4l-utils-" version ".tar.bz2"))
|
||||
(sha256
|
||||
(base32
|
||||
"0cqv8drw0z0kfmz4f50a8kzbrz6vbj6j6q78030hgshr7yq1jqig"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:configure-flags
|
||||
(list (string-append "--with-udevdir="
|
||||
(assoc-ref %outputs "out")
|
||||
"/lib/udev"))))
|
||||
(native-inputs
|
||||
`(("pkg-config" ,pkg-config)))
|
||||
(inputs
|
||||
`(("alsa-lib" ,alsa-lib)
|
||||
("glu" ,glu)
|
||||
("libjpeg" ,libjpeg)
|
||||
("libx11" ,libx11)
|
||||
("qt" ,qt)
|
||||
("eudev" ,eudev)))
|
||||
(synopsis "Realtime video capture utilities for Linux")
|
||||
(description "The v4l-utils provide a series of libraries and utilities to
|
||||
be used for realtime video capture via Linux-specific APIs.")
|
||||
(home-page "https://linuxtv.org/wiki/index.php/V4l-utils")
|
||||
;; libv4l2 is LGPL2.1+, while utilities are GPL2 only.
|
||||
(license (list license:lgpl2.1+ license:gpl2))))
|
||||
|
||||
(define-public obs
|
||||
(package
|
||||
(name "obs")
|
||||
|
|
@ -1293,6 +1326,7 @@ tools, XML authoring components, and an extensible plug-in based API.")
|
|||
("mesa" ,mesa)
|
||||
("pulseaudio" ,pulseaudio)
|
||||
("qt" ,qt)
|
||||
("v4l-utils" ,v4l-utils)
|
||||
("zlib" ,zlib)))
|
||||
(synopsis "Live streaming software")
|
||||
(description "Open Broadcaster Software provides a graphical interface for
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
;;; Copyright © 2014 Sree Harsha Totakura <sreeharsha@totakura.in>
|
||||
;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
|
||||
;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
|
||||
;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -293,7 +293,7 @@ ogginfo, to obtain information (tags, bitrate, length, etc.) about
|
|||
(define opus
|
||||
(package
|
||||
(name "opus")
|
||||
(version "1.1.1")
|
||||
(version "1.1.2")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
|
|
@ -301,7 +301,7 @@ ogginfo, to obtain information (tags, bitrate, length, etc.) about
|
|||
".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"07iplfwim26b6k1bqjyciaqvihps9rk5gi8385axa83ppmbgz14v"))))
|
||||
"1z87x5c5x951lhnm70iqr2gqn15wns5cqsw8nnkvl48jwdw00a8f"))))
|
||||
(build-system gnu-build-system)
|
||||
(synopsis "Versatile audio codec")
|
||||
(description
|
||||
|
|
@ -349,7 +349,7 @@ decoding .opus files.")
|
|||
(define opusfile
|
||||
(package
|
||||
(name "opusfile")
|
||||
(version "0.6")
|
||||
(version "0.7")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
|
|
@ -357,7 +357,7 @@ decoding .opus files.")
|
|||
".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"19iys2kld75k0210b807i4illrdmj3cmmnrgxlc9y4vf6mxp2a14"))))
|
||||
"00f3wwjv3hxwg05g22s6mkkxikz80ljsn70g39cmi43jph9ysawy"))))
|
||||
(build-system gnu-build-system)
|
||||
(propagated-inputs
|
||||
`(("opus" ,opus)))
|
||||
|
|
@ -409,7 +409,7 @@ things in between.")
|
|||
(define-public libshout
|
||||
(package
|
||||
(name "libshout")
|
||||
(version "2.3.1")
|
||||
(version "2.4.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
|
|
@ -417,7 +417,7 @@ things in between.")
|
|||
name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0vlj4dxfxg06xhvv0z2zjjlrjh5di2m28w7v16zcygsy99mmyg6g"))))
|
||||
"0kgjpf8jkgyclw11nilxi8vyjk4s8878x23qyxnvybbgqbgbib7k"))))
|
||||
(build-system gnu-build-system)
|
||||
(native-inputs
|
||||
`(("pkg-config" ,pkg-config)))
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -26,7 +26,8 @@
|
|||
#:use-module (gnu packages admin)
|
||||
#:use-module (guix records)
|
||||
#:use-module (guix gexp)
|
||||
#:export (avahi-service))
|
||||
#:export (avahi-service
|
||||
avahi-service-type))
|
||||
|
||||
;;; Commentary:
|
||||
;;;
|
||||
|
|
|
|||
|
|
@ -79,6 +79,7 @@
|
|||
operating-system-locale-libcs
|
||||
operating-system-mapped-devices
|
||||
operating-system-file-systems
|
||||
operating-system-store-file-system
|
||||
operating-system-activation-script
|
||||
|
||||
operating-system-derivation
|
||||
|
|
@ -678,12 +679,34 @@ listed in OS. The C library expects to find it under
|
|||
(package-version kernel)
|
||||
" (alpha)"))
|
||||
|
||||
(define (store-file-system file-systems)
|
||||
"Return the file system object among FILE-SYSTEMS that contains the store."
|
||||
(match (filter (lambda (fs)
|
||||
(and (file-system-mount? fs)
|
||||
(not (memq 'bind-mount (file-system-flags fs)))
|
||||
(string-prefix? (file-system-mount-point fs)
|
||||
(%store-prefix))))
|
||||
file-systems)
|
||||
((and candidates (head . tail))
|
||||
(reduce (lambda (fs1 fs2)
|
||||
(if (> (string-length (file-system-mount-point fs1))
|
||||
(string-length (file-system-mount-point fs2)))
|
||||
fs1
|
||||
fs2))
|
||||
head
|
||||
candidates))))
|
||||
|
||||
(define (operating-system-store-file-system os)
|
||||
"Return the file system that contains the store of OS."
|
||||
(store-file-system (operating-system-file-systems os)))
|
||||
|
||||
(define* (operating-system-grub.cfg os #:optional (old-entries '()))
|
||||
"Return the GRUB configuration file for OS. Use OLD-ENTRIES to populate the
|
||||
\"old entries\" menu."
|
||||
(mlet* %store-monad
|
||||
((system (operating-system-derivation os))
|
||||
(root-fs -> (operating-system-root-file-system os))
|
||||
(store-fs -> (operating-system-store-file-system os))
|
||||
(kernel -> (operating-system-kernel os))
|
||||
(root-device -> (if (eq? 'uuid (file-system-title root-fs))
|
||||
(uuid->string (file-system-device root-fs))
|
||||
|
|
@ -698,7 +721,8 @@ listed in OS. The C library expects to find it under
|
|||
"/boot")
|
||||
(operating-system-kernel-arguments os)))
|
||||
(initrd #~(string-append #$system "/initrd"))))))
|
||||
(grub-configuration-file (operating-system-bootloader os) entries
|
||||
(grub-configuration-file (operating-system-bootloader os)
|
||||
store-fs entries
|
||||
#:old-entries old-entries)))
|
||||
|
||||
(define (operating-system-parameters-file os)
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -25,6 +25,7 @@
|
|||
#:use-module (guix gexp)
|
||||
#:use-module (guix download)
|
||||
#:use-module (gnu artwork)
|
||||
#:use-module (gnu system file-systems)
|
||||
#:autoload (gnu packages grub) (grub)
|
||||
#:autoload (gnu packages inkscape) (inkscape)
|
||||
#:autoload (gnu packages imagemagick) (imagemagick)
|
||||
|
|
@ -153,10 +154,12 @@ WIDTH/HEIGHT, or #f if none was found."
|
|||
(with-monad %store-monad
|
||||
(return #f)))))
|
||||
|
||||
(define (eye-candy config system port)
|
||||
(define (eye-candy config root-fs system port)
|
||||
"Return in %STORE-MONAD a gexp that writes to PORT (a port-valued gexp) the
|
||||
'grub.cfg' part concerned with graphics mode, background images, colors, and
|
||||
all that."
|
||||
all that. ROOT-FS is a file-system object denoting the root file system where
|
||||
the store is. SYSTEM must be the target system string---e.g.,
|
||||
\"x86_64-linux\"."
|
||||
(define setup-gfxterm-body
|
||||
;; Intel systems need to be switched into graphics mode, whereas most
|
||||
;; other modern architectures have no other mode and therefore don't need
|
||||
|
|
@ -179,15 +182,18 @@ all that."
|
|||
(string-append (symbol->string (assoc-ref colors 'fg)) "/"
|
||||
(symbol->string (assoc-ref colors 'bg)))))
|
||||
|
||||
(define font-file
|
||||
#~(string-append #$grub "/share/grub/unicode.pf2"))
|
||||
|
||||
(mlet* %store-monad ((image (grub-background-image config)))
|
||||
(return (and image
|
||||
#~(format #$port "
|
||||
function setup_gfxterm {~a}
|
||||
|
||||
# Set 'root' to the partition that contains /gnu/store.
|
||||
search --file --set ~a/share/grub/unicode.pf2
|
||||
~a
|
||||
|
||||
if loadfont ~a/share/grub/unicode.pf2; then
|
||||
if loadfont ~a; then
|
||||
setup_gfxterm
|
||||
fi
|
||||
|
||||
|
|
@ -200,7 +206,9 @@ else
|
|||
set menu_color_highlight=white/blue
|
||||
fi~%"
|
||||
#$setup-gfxterm-body
|
||||
#$grub #$grub
|
||||
#$(grub-root-search root-fs font-file)
|
||||
#$font-file
|
||||
|
||||
#$image
|
||||
#$(theme-colors grub-theme-color-normal)
|
||||
#$(theme-colors grub-theme-color-highlight))))))
|
||||
|
|
@ -210,13 +218,31 @@ fi~%"
|
|||
;;; Configuration file.
|
||||
;;;
|
||||
|
||||
(define* (grub-configuration-file config entries
|
||||
(define (grub-root-search root-fs file)
|
||||
"Return the GRUB 'search' command to look for ROOT-FS, which contains FILE,
|
||||
a gexp. The result is a gexp that can be inserted in the grub.cfg-generation
|
||||
code."
|
||||
(case (file-system-title root-fs)
|
||||
;; Preferably refer to ROOT-FS by its UUID or label. This is more
|
||||
;; efficient and less ambiguous, see <>.
|
||||
((uuid)
|
||||
(format #f "search --fs-uuid --set ~a"
|
||||
(uuid->string (file-system-device root-fs))))
|
||||
((label)
|
||||
(format #f "search --label --set ~a"
|
||||
(file-system-device root-fs)))
|
||||
(else
|
||||
;; As a last resort, look for any device containing FILE.
|
||||
#~(format #f "search --file --set ~a" #$file))))
|
||||
|
||||
(define* (grub-configuration-file config store-fs entries
|
||||
#:key
|
||||
(system (%current-system))
|
||||
(old-entries '()))
|
||||
"Return the GRUB configuration file corresponding to CONFIG, a
|
||||
<grub-configuration> object. OLD-ENTRIES is taken to be a list of menu
|
||||
entries corresponding to old generations of the system."
|
||||
<grub-configuration> object, and where the store is available at STORE-FS, a
|
||||
<file-system> object. OLD-ENTRIES is taken to be a list of menu entries
|
||||
corresponding to old generations of the system."
|
||||
(define linux-image-name
|
||||
(if (string-prefix? "mips" system)
|
||||
"vmlinuz"
|
||||
|
|
@ -229,18 +255,18 @@ entries corresponding to old generations of the system."
|
|||
(match-lambda
|
||||
(($ <menu-entry> label linux arguments initrd)
|
||||
#~(format port "menuentry ~s {
|
||||
# Set 'root' to the partition that contains the kernel.
|
||||
search --file --set ~a/~a~%
|
||||
|
||||
~a
|
||||
linux ~a/~a ~a
|
||||
initrd ~a
|
||||
}~%"
|
||||
#$label
|
||||
#$linux #$linux-image-name
|
||||
#$(grub-root-search store-fs
|
||||
#~(string-append #$linux "/"
|
||||
#$linux-image-name))
|
||||
#$linux #$linux-image-name (string-join (list #$@arguments))
|
||||
#$initrd))))
|
||||
|
||||
(mlet %store-monad ((sugar (eye-candy config system #~port)))
|
||||
(mlet %store-monad ((sugar (eye-candy config store-fs system #~port)))
|
||||
(define builder
|
||||
#~(call-with-output-file #$output
|
||||
(lambda (port)
|
||||
|
|
|
|||
|
|
@ -29,12 +29,14 @@
|
|||
#:use-module (guix base32)
|
||||
#:use-module ((guix download) #:select (download-to-store))
|
||||
#:use-module (guix import utils)
|
||||
#:use-module ((guix build-system r) #:select (cran-uri))
|
||||
#:use-module ((guix build-system r) #:select (cran-uri bioconductor-uri))
|
||||
#:use-module (guix upstream)
|
||||
#:use-module (guix packages)
|
||||
#:use-module (gnu packages)
|
||||
#:export (cran->guix-package
|
||||
%cran-updater))
|
||||
bioconductor->guix-package
|
||||
%cran-updater
|
||||
%bioconductor-updater))
|
||||
|
||||
;;; Commentary:
|
||||
;;;
|
||||
|
|
@ -108,6 +110,15 @@ package definition."
|
|||
`((,type (,'quasiquote ,(format-inputs package-inputs)))))))
|
||||
|
||||
(define %cran-url "http://cran.r-project.org/web/packages/")
|
||||
(define %bioconductor-url "http://bioconductor.org/packages/")
|
||||
|
||||
;; The latest Bioconductor release is 3.2. Bioconductor packages should be
|
||||
;; updated together.
|
||||
(define %bioconductor-svn-url
|
||||
(string-append "https://readonly:readonly@"
|
||||
"hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/"
|
||||
"madman/Rpacks/"))
|
||||
|
||||
|
||||
(define (fetch-description base-url name)
|
||||
"Return an alist of the contents of the DESCRIPTION file for the R package
|
||||
|
|
@ -136,24 +147,31 @@ empty list when the FIELD cannot be found."
|
|||
(string-any char-set:whitespace item)))
|
||||
(map string-trim-both items))))))
|
||||
|
||||
(define (description->package meta)
|
||||
"Return the `package' s-expression for a CRAN package from the alist META,
|
||||
which was derived from the R package's DESCRIPTION file."
|
||||
(define (description->package repository meta)
|
||||
"Return the `package' s-expression for an R package published on REPOSITORY
|
||||
from the alist META, which was derived from the R package's DESCRIPTION file."
|
||||
(define (guix-name name)
|
||||
(if (string-prefix? "r-" name)
|
||||
(string-downcase name)
|
||||
(string-append "r-" (string-downcase name))))
|
||||
|
||||
(let* ((name (assoc-ref meta "Package"))
|
||||
(let* ((base-url (case repository
|
||||
((cran) %cran-url)
|
||||
((bioconductor) %bioconductor-url)))
|
||||
(uri-helper (case repository
|
||||
((cran) cran-uri)
|
||||
((bioconductor) bioconductor-uri)))
|
||||
(name (assoc-ref meta "Package"))
|
||||
(synopsis (assoc-ref meta "Title"))
|
||||
(version (assoc-ref meta "Version"))
|
||||
(license (string->license (assoc-ref meta "License")))
|
||||
;; Some packages have multiple home pages. Some have none.
|
||||
(home-page (match (listify meta "URL")
|
||||
((url rest ...) url)
|
||||
(_ (string-append %cran-url name))))
|
||||
(source-url (match (cran-uri name version)
|
||||
(_ (string-append base-url name))))
|
||||
(source-url (match (uri-helper name version)
|
||||
((url rest ...) url)
|
||||
((? string? url) url)
|
||||
(_ #f)))
|
||||
(tarball (with-store store (download-to-store store source-url)))
|
||||
(sysdepends (map string-downcase (listify meta "SystemRequirements")))
|
||||
|
|
@ -167,26 +185,32 @@ which was derived from the R package's DESCRIPTION file."
|
|||
(version ,version)
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri ,name version))
|
||||
(uri (,(procedure-name uri-helper) ,name version))
|
||||
(sha256
|
||||
(base32
|
||||
,(bytevector->nix-base32-string (file-sha256 tarball))))))
|
||||
(properties ,`(,'quasiquote ((,'upstream-name . ,name))))
|
||||
,@(if (not (equal? (string-append "r-" name)
|
||||
(guix-name name)))
|
||||
`((properties ,`(,'quasiquote ((,'upstream-name . ,name)))))
|
||||
'())
|
||||
(build-system r-build-system)
|
||||
,@(maybe-inputs sysdepends)
|
||||
,@(maybe-inputs propagate 'propagated-inputs)
|
||||
(home-page ,(if (string-null? home-page)
|
||||
(string-append %cran-url name)
|
||||
(string-append base-url name)
|
||||
home-page))
|
||||
(synopsis ,synopsis)
|
||||
(description ,(beautify-description (assoc-ref meta "Description")))
|
||||
(license ,license))))
|
||||
|
||||
(define (cran->guix-package package-name)
|
||||
"Fetch the metadata for PACKAGE-NAME from cran.r-project.org, and return the
|
||||
`package' s-expression corresponding to that package, or #f on failure."
|
||||
(let ((module-meta (fetch-description %cran-url package-name)))
|
||||
(and=> module-meta description->package)))
|
||||
(define* (cran->guix-package package-name #:optional (repo 'cran))
|
||||
"Fetch the metadata for PACKAGE-NAME from REPO and return the `package'
|
||||
s-expression corresponding to that package, or #f on failure."
|
||||
(let* ((url (case repo
|
||||
((cran) %cran-url)
|
||||
((bioconductor) %bioconductor-svn-url)))
|
||||
(module-meta (fetch-description url package-name)))
|
||||
(and=> module-meta (cut description->package repo <>))))
|
||||
|
||||
|
||||
;;;
|
||||
|
|
@ -212,7 +236,7 @@ which was derived from the R package's DESCRIPTION file."
|
|||
(_ #f)))
|
||||
(_ #f)))))
|
||||
|
||||
(define (latest-release package)
|
||||
(define (latest-cran-release package)
|
||||
"Return an <upstream-source> for the latest release of PACKAGE."
|
||||
|
||||
(define upstream-name
|
||||
|
|
@ -229,16 +253,55 @@ which was derived from the R package's DESCRIPTION file."
|
|||
(version version)
|
||||
(urls (cran-uri upstream-name version))))))
|
||||
|
||||
(define (latest-bioconductor-release package)
|
||||
"Return an <upstream-source> for the latest release of PACKAGE."
|
||||
|
||||
(define upstream-name
|
||||
(package->upstream-name (specification->package package)))
|
||||
|
||||
(define meta
|
||||
(fetch-description %bioconductor-svn-url upstream-name))
|
||||
|
||||
(and meta
|
||||
(let ((version (assoc-ref meta "Version")))
|
||||
;; Bioconductor does not provide signatures.
|
||||
(upstream-source
|
||||
(package package)
|
||||
(version version)
|
||||
(urls (bioconductor-uri upstream-name version))))))
|
||||
|
||||
(define (cran-package? package)
|
||||
"Return true if PACKAGE is an R package from CRAN."
|
||||
;; Assume all R packages are available on CRAN.
|
||||
(string-prefix? "r-" (package-name package)))
|
||||
(and (string-prefix? "r-" (package-name package))
|
||||
(match (and=> (package-source package) origin-uri)
|
||||
((? string? uri)
|
||||
(string-prefix? "mirror://cran" uri))
|
||||
((? list? uris)
|
||||
(any (cut string-prefix? "mirror://cran" <>) uris))
|
||||
(_ #f))))
|
||||
|
||||
(define (bioconductor-package? package)
|
||||
"Return true if PACKAGE is an R package from Bioconductor."
|
||||
(and (string-prefix? "r-" (package-name package))
|
||||
(match (and=> (package-source package) origin-uri)
|
||||
((? string? uri)
|
||||
(string-prefix? "http://bioconductor.org" uri))
|
||||
((? list? uris)
|
||||
(any (cut string-prefix? "http://bioconductor.org" <>) uris))
|
||||
(_ #f))))
|
||||
|
||||
(define %cran-updater
|
||||
(upstream-updater
|
||||
(name 'cran)
|
||||
(description "Updater for CRAN packages")
|
||||
(pred cran-package?)
|
||||
(latest latest-release)))
|
||||
(latest latest-cran-release)))
|
||||
|
||||
(define %bioconductor-updater
|
||||
(upstream-updater
|
||||
(name 'bioconductor)
|
||||
(description "Updater for Bioconductor packages")
|
||||
(pred bioconductor-package?)
|
||||
(latest latest-bioconductor-release)))
|
||||
|
||||
;;; cran.scm ends here
|
||||
|
|
|
|||
|
|
@ -77,7 +77,7 @@ the package."
|
|||
(bytevector-u8-set! bv i (read-byte i))
|
||||
(loop (1+ i)))))))
|
||||
|
||||
(define (make-gem-sexp name version hash home-page description
|
||||
(define (make-gem-sexp name version hash home-page synopsis description
|
||||
dependencies licenses)
|
||||
"Return the `package' s-expression for a Ruby package with the given NAME,
|
||||
VERSION, HASH, HOME-PAGE, DESCRIPTION, DEPENDENCIES, and LICENSES."
|
||||
|
|
@ -101,7 +101,7 @@ VERSION, HASH, HOME-PAGE, DESCRIPTION, DEPENDENCIES, and LICENSES."
|
|||
(,'unquote
|
||||
,(string->symbol name))))
|
||||
dependencies)))))
|
||||
(synopsis ,description) ; nothing better to use
|
||||
(synopsis ,synopsis)
|
||||
(description ,description)
|
||||
(home-page ,home-page)
|
||||
(license ,(match licenses
|
||||
|
|
@ -117,6 +117,7 @@ VERSION, HASH, HOME-PAGE, DESCRIPTION, DEPENDENCIES, and LICENSES."
|
|||
(let ((name (assoc-ref package "name"))
|
||||
(version (assoc-ref package "version"))
|
||||
(hash (assoc-ref package "sha"))
|
||||
(synopsis (assoc-ref package "info")) ; nothing better to use
|
||||
(description (beautify-description
|
||||
(assoc-ref package "info")))
|
||||
(home-page (assoc-ref package "homepage_uri"))
|
||||
|
|
@ -129,5 +130,5 @@ VERSION, HASH, HOME-PAGE, DESCRIPTION, DEPENDENCIES, and LICENSES."
|
|||
"runtime")))
|
||||
(licenses (map string->license
|
||||
(assoc-ref package "licenses"))))
|
||||
(make-gem-sexp name version hash home-page
|
||||
(make-gem-sexp name version hash home-page synopsis
|
||||
description dependencies licenses)))))
|
||||
|
|
|
|||
|
|
@ -4,6 +4,7 @@
|
|||
;;; Copyright © 2012, 2013 Nikita Karetnikov <nikita@karetnikov.org>
|
||||
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
|
||||
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -49,7 +50,7 @@
|
|||
imlib2
|
||||
ipa
|
||||
lgpl2.0 lgpl2.0+ lgpl2.1 lgpl2.1+ lgpl3 lgpl3+
|
||||
mpl1.1 mpl2.0
|
||||
mpl1.0 mpl1.1 mpl2.0
|
||||
ms-pl
|
||||
ncsa
|
||||
openldap2.8 openssl
|
||||
|
|
@ -302,6 +303,11 @@ at URI, which may be a file:// URI pointing the package's tree."
|
|||
"https://www.gnu.org/licenses/lgpl.html"
|
||||
"https://www.gnu.org/licenses/license-list#LGPLv3"))
|
||||
|
||||
(define mpl1.0
|
||||
(license "MPL 1.0"
|
||||
"http://www.mozilla.org/MPL/1.0/"
|
||||
"https://www.gnu.org/licenses/license-list.html#MPL"))
|
||||
|
||||
(define mpl1.1
|
||||
(license "MPL 1.1"
|
||||
"http://directory.fsf.org/wiki/License:MPLv1.1"
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2012, 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2013 Mark H Weaver <mhw@netris.org>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
|
|
@ -153,6 +153,8 @@ options handled by 'set-build-options-from-command-line', and listed in
|
|||
(display (_ "
|
||||
-K, --keep-failed keep build tree of failed builds"))
|
||||
(display (_ "
|
||||
-k, --keep-going keep going when some of the derivations fail"))
|
||||
(display (_ "
|
||||
-n, --dry-run do not build the derivations"))
|
||||
(display (_ "
|
||||
--fallback fall back to building when the substituter fails"))
|
||||
|
|
@ -183,6 +185,7 @@ options handled by 'set-build-options-from-command-line', and listed in
|
|||
;; TODO: Add more options.
|
||||
(set-build-options store
|
||||
#:keep-failed? (assoc-ref opts 'keep-failed?)
|
||||
#:keep-going? (assoc-ref opts 'keep-going?)
|
||||
#:rounds (assoc-ref opts 'rounds)
|
||||
#:build-cores (or (assoc-ref opts 'cores) 0)
|
||||
#:max-build-jobs (or (assoc-ref opts 'max-jobs) 1)
|
||||
|
|
@ -214,6 +217,11 @@ options handled by 'set-build-options-from-command-line', and listed in
|
|||
(apply values
|
||||
(alist-cons 'keep-failed? #t result)
|
||||
rest)))
|
||||
(option '(#\k "keep-going") #f #f
|
||||
(lambda (opt name arg result . rest)
|
||||
(apply values
|
||||
(alist-cons 'keep-going? #t result)
|
||||
rest)))
|
||||
(option '("rounds") #t #f
|
||||
(lambda (opt name arg result . rest)
|
||||
(apply values
|
||||
|
|
|
|||
|
|
@ -41,6 +41,8 @@
|
|||
(define (show-help)
|
||||
(display (_ "Usage: guix import cran PACKAGE-NAME
|
||||
Import and convert the CRAN package for PACKAGE-NAME.\n"))
|
||||
(display (_ "
|
||||
-a, --archive=ARCHIVE specify the archive repository"))
|
||||
(display (_ "
|
||||
-h, --help display this help and exit"))
|
||||
(display (_ "
|
||||
|
|
@ -57,6 +59,10 @@ Import and convert the CRAN package for PACKAGE-NAME.\n"))
|
|||
(option '(#\V "version") #f #f
|
||||
(lambda args
|
||||
(show-version-and-exit "guix import cran")))
|
||||
(option '(#\a "archive") #t #f
|
||||
(lambda (opt name arg result)
|
||||
(alist-cons 'repo (string->symbol arg)
|
||||
(alist-delete 'repo result))))
|
||||
%standard-import-options))
|
||||
|
||||
|
||||
|
|
@ -82,7 +88,8 @@ Import and convert the CRAN package for PACKAGE-NAME.\n"))
|
|||
(reverse opts))))
|
||||
(match args
|
||||
((package-name)
|
||||
(let ((sexp (cran->guix-package package-name)))
|
||||
(let ((sexp (cran->guix-package package-name
|
||||
(or (assoc-ref opts 'repo) 'cran))))
|
||||
(unless sexp
|
||||
(leave (_ "failed to download description for package '~a'~%")
|
||||
package-name))
|
||||
|
|
|
|||
|
|
@ -195,6 +195,7 @@ unavailable optional dependencies such as Guile-JSON."
|
|||
%gnome-updater
|
||||
%elpa-updater
|
||||
%cran-updater
|
||||
%bioconductor-updater
|
||||
((guix import pypi) => %pypi-updater)))
|
||||
|
||||
(define (lookup-updater name)
|
||||
|
|
|
|||
|
|
@ -86,16 +86,6 @@ Date/Publication: 2015-07-14 14:15:16
|
|||
'()
|
||||
((@@ (guix import cran) listify) simple-alist "BadList"))
|
||||
|
||||
(test-equal "beautify-description: use double spacing"
|
||||
"This is a package. It is great. Trust me Mr. Hendrix."
|
||||
((@@ (guix import cran) beautify-description)
|
||||
"This is a package. It is great. Trust me Mr. Hendrix."))
|
||||
|
||||
(test-equal "beautify-description: transform fragment into sentence"
|
||||
"This package provides a function to establish world peace"
|
||||
((@@ (guix import cran) beautify-description)
|
||||
"A function to establish world peace"))
|
||||
|
||||
(test-assert "description->package"
|
||||
;; Replace network resources with sample data.
|
||||
(mock ((guix build download) url-fetch
|
||||
|
|
@ -107,7 +97,7 @@ Date/Publication: 2015-07-14 14:15:16
|
|||
("mirror://cran/src/contrib/My-Example_1.2.3.tar.gz"
|
||||
"source")
|
||||
(_ (error "Unexpected URL: " url))))))))
|
||||
(match ((@@ (guix import cran) description->package) description-alist)
|
||||
(match ((@@ (guix import cran) description->package) 'cran description-alist)
|
||||
(('package
|
||||
('name "r-my-example")
|
||||
('version "1.2.3")
|
||||
|
|
|
|||
|
|
@ -151,6 +151,33 @@
|
|||
;; the contents.
|
||||
(valid-path? %store (derivation->output-path drv)))))
|
||||
|
||||
(test-assert "derivation fails but keep going"
|
||||
;; In keep-going mode, 'build-derivations' should fail because of D1, but it
|
||||
;; must return only after D2 has succeeded.
|
||||
(with-store store
|
||||
(let* ((d1 (derivation %store "fails"
|
||||
%bash `("-c" "false")
|
||||
#:inputs `((,%bash))))
|
||||
(d2 (build-expression->derivation %store "sleep-then-succeed"
|
||||
`(begin
|
||||
,(random-text)
|
||||
;; XXX: Hopefully that's long
|
||||
;; enough that D1 has already
|
||||
;; failed.
|
||||
(sleep 2)
|
||||
(mkdir %output)))))
|
||||
(set-build-options %store
|
||||
#:use-substitutes? #f
|
||||
#:keep-going? #t)
|
||||
(guard (c ((nix-protocol-error? c)
|
||||
(and (= 100 (nix-protocol-error-status c))
|
||||
(string-contains (nix-protocol-error-message c)
|
||||
(derivation-file-name d1))
|
||||
(not (valid-path? %store (derivation->output-path d1)))
|
||||
(valid-path? %store (derivation->output-path d2)))))
|
||||
(build-derivations %store (list d1 d2))
|
||||
#f))))
|
||||
|
||||
(test-assert "identical files are deduplicated"
|
||||
(let* ((build1 (add-text-to-store %store "one.sh"
|
||||
"echo hello, world > \"$out\"\n"
|
||||
|
|
|
|||
|
|
@ -69,7 +69,7 @@
|
|||
(("bundler" ('unquote 'bundler))
|
||||
("ruby-bar" ('unquote 'ruby-bar)))))
|
||||
('synopsis "A cool gem")
|
||||
('description "A cool gem")
|
||||
('description "This package provides a cool gem")
|
||||
('home-page "https://example.com")
|
||||
('license ('list 'expat 'asl2.0)))
|
||||
#t)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,39 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
||||
;;; under the terms of the GNU General Public License as published by
|
||||
;;; the Free Software Foundation; either version 3 of the License, or (at
|
||||
;;; your option) any later version.
|
||||
;;;
|
||||
;;; GNU Guix is distributed in the hope that it will be useful, but
|
||||
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
;;; GNU General Public License for more details.
|
||||
;;;
|
||||
;;; You should have received a copy of the GNU General Public License
|
||||
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
(define-module (test-import-utils)
|
||||
#:use-module (guix tests)
|
||||
#:use-module (guix import utils)
|
||||
#:use-module (srfi srfi-64))
|
||||
|
||||
(test-begin "import-utils")
|
||||
|
||||
(test-equal "beautify-description: use double spacing"
|
||||
"This is a package. It is great. Trust me Mr. Hendrix."
|
||||
(beautify-description
|
||||
"This is a package. It is great. Trust me Mr. Hendrix."))
|
||||
|
||||
(test-equal "beautify-description: transform fragment into sentence"
|
||||
"This package provides a function to establish world peace"
|
||||
(beautify-description "A function to establish world peace"))
|
||||
|
||||
(test-end "import-utils")
|
||||
|
||||
|
||||
(exit (= (test-runner-fail-count (test-runner-current)) 0))
|
||||
|
|
@ -1,7 +1,7 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2012, 2013 Cyril Roelandt <tipecaml@gmail.com>
|
||||
;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org>
|
||||
;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
|
|
@ -19,6 +19,9 @@
|
|||
;;; You should have received a copy of the GNU General Public License
|
||||
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
;; Avoid interference.
|
||||
(unsetenv "http_proxy")
|
||||
|
||||
(define-module (test-lint)
|
||||
#:use-module (guix tests)
|
||||
#:use-module (guix download)
|
||||
|
|
|
|||
|
|
@ -16,6 +16,9 @@
|
|||
;;; You should have received a copy of the GNU General Public License
|
||||
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
;; Avoid interference.
|
||||
(unsetenv "http_proxy")
|
||||
|
||||
(define-module (test-publish)
|
||||
#:use-module (guix scripts publish)
|
||||
#:use-module (guix tests)
|
||||
|
|
@ -62,6 +65,7 @@
|
|||
(connect conn AF_INET (inet-pton AF_INET "127.0.0.1") 6789))
|
||||
(loop))))
|
||||
|
||||
|
||||
(test-begin "publish")
|
||||
|
||||
(test-equal "/nix-cache-info"
|
||||
|
|
|
|||
|
|
@ -0,0 +1,77 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
||||
;;; under the terms of the GNU General Public License as published by
|
||||
;;; the Free Software Foundation; either version 3 of the License, or (at
|
||||
;;; your option) any later version.
|
||||
;;;
|
||||
;;; GNU Guix is distributed in the hope that it will be useful, but
|
||||
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
;;; GNU General Public License for more details.
|
||||
;;;
|
||||
;;; You should have received a copy of the GNU General Public License
|
||||
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
(define-module (test-system)
|
||||
#:use-module (gnu)
|
||||
#:use-module (guix store)
|
||||
#:use-module (srfi srfi-1)
|
||||
#:use-module (srfi srfi-64))
|
||||
|
||||
;; Test the (gnu system) module.
|
||||
|
||||
(define %root-fs
|
||||
(file-system
|
||||
(device "my-root")
|
||||
(title 'label)
|
||||
(mount-point "/")
|
||||
(type "ext4")))
|
||||
|
||||
(define %os
|
||||
(operating-system
|
||||
(host-name "komputilo")
|
||||
(timezone "Europe/Berlin")
|
||||
(locale "en_US.utf8")
|
||||
(bootloader (grub-configuration (device "/dev/sdX")))
|
||||
(file-systems (cons %root-fs %base-file-systems))
|
||||
|
||||
(users %base-user-accounts)))
|
||||
|
||||
(test-begin "system")
|
||||
|
||||
(test-assert "operating-system-store-file-system"
|
||||
;; %BASE-FILE-SYSTEMS defines a bind-mount for /gnu/store, but this
|
||||
;; shouldn't be a problem.
|
||||
(eq? %root-fs
|
||||
(operating-system-store-file-system %os)))
|
||||
|
||||
(test-assert "operating-system-store-file-system, prefix"
|
||||
(let* ((gnu (file-system
|
||||
(device "foobar")
|
||||
(mount-point (dirname (%store-prefix)))
|
||||
(type "ext5")))
|
||||
(os (operating-system
|
||||
(inherit %os)
|
||||
(file-systems (cons* gnu %root-fs
|
||||
%base-file-systems)))))
|
||||
(eq? gnu (operating-system-store-file-system os))))
|
||||
|
||||
(test-assert "operating-system-store-file-system, store"
|
||||
(let* ((gnu (file-system
|
||||
(device "foobar")
|
||||
(mount-point (%store-prefix))
|
||||
(type "ext5")))
|
||||
(os (operating-system
|
||||
(inherit %os)
|
||||
(file-systems (cons* gnu %root-fs
|
||||
%base-file-systems)))))
|
||||
(eq? gnu (operating-system-store-file-system os))))
|
||||
|
||||
(test-end)
|
||||
|
||||
|
||||
(exit (= (test-runner-fail-count (test-runner-current)) 0))
|
||||
Reference in New Issue