Ben Woodcroft writes:
>> +;; TopHat is released under the Boost Software License, Version 1.0
>> +;; See
>> https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
>> +(license (license:x11-style "http://www.boost.org/LICENSE_1_0.txt";
>> +
Ludovic Courtès writes:
> Ricardo Wurmus skribis:
>
>> +(synopsis "Spliced read mapper for RNA-Seq")
>> +(description
>> + "TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns
>
> It would be nice to contextualize a bit, for instance by adding a word
> after “RNA-S
Ludovic Courtès writes:
> Ricardo Wurmus skribis:
>
>> From e7090b086c71fb8f8a56b6c7cb078b94bc577d2c Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus
>> Date: Tue, 19 Jan 2016 16:04:01 +0100
>> Subject: [PATCH 1/2] gnu: star: Use "modify-phases" syntax.
>>
>> * gnu/packages/bioinformatics.scm
Ben Woodcroft writes:
> I notice that 2.5.1a is now released - I guess you started working on
> the patch before it was so.
And now 2.5.1b has been released :) I updated the commit. Thanks for
the hint.
> STARlong is in the binaries that are distributed ie
> https://github.com/alexdobin/ST
Hi,
Seeing as guix is becoming more and more complete, it would be great to
have 'command-not-found' [1] or similar available, so that typing in the
name of an uninstalled binary begets a suggestion on which package(s) to
install, like Ubuntu gives:
$ gitk
The program 'gitk' is currently not
Alex Kost skribis:
> * modules/shepherd/comm.scm (make-dmd-output-port): Rename to...
> (make-shepherd-output-port): ... this.
> (dmd-output-port): Rename to...
> (shepherd-output-port): ... this.
> * modules/shepherd.scm (main): Adjust accordingly.
Applied, thanks!
Ludo’.
On Sat, Jan 23, 2016 at 07:55:37AM +1000, Ben Woodcroft wrote:
>
> On 23/01/16 06:35, Leo Famulari wrote:
> >On Fri, Jan 22, 2016 at 10:12:54PM +1000, Ben Woodcroft wrote:
> [..]
>
> Thanks Leo. As well as responding to your review the attached patch breaks
> out the rRNA databases out into a sep
On 23/01/16 06:35, Leo Famulari wrote:
On Fri, Jan 22, 2016 at 10:12:54PM +1000, Ben Woodcroft wrote:
[..]
Thanks Leo. As well as responding to your review the attached patch
breaks out the rRNA databases out into a separate output "db", removing
73MB from the default package. Is "db" a good
Hi
I tried following the manual build* from a fresh git pull.
From 7.6:
" ./pre-inst-env guix build gnew --keep-failed
If the package is unknown to the ‘guix’ command, it may be that the
source file contains a syntax error, or lacks a ‘define-public’ clause
to export the package variable.
On Fri, Jan 22, 2016 at 10:12:54PM +1000, Ben Woodcroft wrote:
> Thanks in advance as usual.
> From 448c2435e50d9d860f1153934058effa42fc6495 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft
> Date: Sat, 16 Jan 2016 13:33:08 +1000
> Subject: [PATCH] gnu: Add sortmerna.
>
> * gnu/packages/bioinforma
On Thu, Jan 21, 2016 at 04:05:43PM +0100, Ricardo Wurmus wrote:
> From 546a8651db1c420fee841a2da6474593e4c9aa93 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus
> Date: Thu, 21 Jan 2016 16:03:26 +0100
> Subject: [PATCH] gnu: Add Augeas.
>
> * gnu/packages/augeas.scm: New file.
> * gnu-system.am (G
On Thu, Jan 21, 2016 at 10:53:56AM +0200, Efraim Flashner wrote:
> I've been holding on to these for a bit, waiting to integrate them before
> submitting them.
>
> cmocka: This is supposed to be used by mpv for running the tests, but the
> tests fail. Since mpv works I wasn't super motivated to tr
Arr, I missed 2 lines in "halt.scm" and "reboot.scm". Here is the
updated patch.
>From d91b7be586cb2edda6fd67bb6ef44a71bd669149 Mon Sep 17 00:00:00 2001
From: Alex Kost
Date: Fri, 22 Jan 2016 22:19:46 +0300
Subject: [PATCH 3/4] Rename 'dmd' service to 'shepherd'.
* modules/shepherd/service.scm
* modules/shepherd/service.scm (dmd-service): Rename to...
(shepherd-service): ... this. Adjust the rest file accordingly.
* modules/herd.scm: Likewise.
* modules/shepherd.scm: Likewise.
* modules/shepherd/support.scm (make-bare-init-file): Likewise.
* shepherd.texi: Likewise.
* tests/basic.sh: Li
* modules/shepherd/comm.scm (make-dmd-output-port): Rename to...
(make-shepherd-output-port): ... this.
(dmd-output-port): Rename to...
(shepherd-output-port): ... this.
* modules/shepherd.scm (main): Adjust accordingly.
---
modules/shepherd.scm | 2 +-
modules/shepherd/comm.scm | 8
* modules/shepherd/support.scm (make-bare-init-file): Adjust comment
lines for the rename.
---
modules/shepherd/support.scm | 8
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/modules/shepherd/support.scm b/modules/shepherd/support.scm
index f1878a6..369beb8 100644
--- a/
Hello, there are still many 'dmd' instances in the source, so here are
several patches for "dmd -> shepherd" transition. If this is
acceptable, I can continue to get rid of the left "dmd" things.
[PATCH 1/4] Rename 'dmd-output-port' to 'shepherd-output-port'.
[PATCH 2/4] Rename 'dmd-command' to '
* modules/shepherd/comm.scm (): Rename record type and its
accessors to...
(): ... this.
(read-command, write-command): Adjust accordingly.
* modules/halt.scm (main): Likewise.
* modules/herd.scm (run-command): Likewise.
* modules/reboot.scm (main): Likewise.
* modules/shepherd.scm (process-command
On Fri, Jan 22, 2016 at 06:15:11PM +0100, Ludovic Courtès wrote:
> Leo Famulari skribis:
>
> > * gnu/packages/bittorrent.scm (transmission)[inputs]: Add
> > adwaita-icon-theme and hicolor-icon-theme.
>
> I don’t think we should take that route, because we would end up doing
> that for each and e
Thanks.
On Fri, Jan 22, 2016 at 07:24:49PM +0100, Ricardo Wurmus wrote:
>
> Ludovic Courtès writes:
>
> > Pjotr Prins skribis:
> >
> >> * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4
> >
> > In fact this has already been pushed.
>
> I did this (after adding a missing period), but
Ludovic Courtès writes:
> Pjotr Prins skribis:
>
>> * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4
>
> In fact this has already been pushed.
I did this (after adding a missing period), but forgot to reply on the
mailing list.
~~ Ricardo
Pjotr Prins skribis:
> * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4
In fact this has already been pushed.
Ludo’.
Pjotr Prins skribis:
> Anyone care to push this?
Please, be more patient. If you’ve seen the amount of stuff to be
reviewed, discussed, etc., that’s taking a lot of the time of a few
people. So yes, it can take more than a day before you get feedback.
The good news is that everyone can help b
Leo Famulari skribis:
> * gnu/packages/bittorrent.scm (transmission)[inputs]: Add
> adwaita-icon-theme and hicolor-icon-theme.
I don’t think we should take that route, because we would end up doing
that for each and every GTK+ package.
However, we could:
1. On GuixSD, arrange so that these t
Eric Bavier skribis:
> On 2016-01-17 14:48, l...@gnu.org wrote:
>> Mark H Weaver skribis:
>>
>>> Many haskell package builds are failing on core-updates:
>>>
>>> http://hydra.gnu.org/eval/108790?filter=ghc
>>>
>>> We see this error in many cases:
>>>
>>> ERROR: In procedure regexp-exec: Wron
Andreas Enge skribis:
> On Thu, Jan 21, 2016 at 09:48:58PM +0100, Ludovic Courtès wrote:
>> Could be. OTOH, there’s a risk of Doxygen being effectively “broken by
>> default” if, as I presume, many programs expect it to be able to
>> generate PNGs for class diagrams.
>
> Okay. As propagated inpu
Ricardo Wurmus skribis:
> From e7090b086c71fb8f8a56b6c7cb078b94bc577d2c Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus
> Date: Tue, 19 Jan 2016 16:04:01 +0100
> Subject: [PATCH 1/2] gnu: star: Use "modify-phases" syntax.
>
> * gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phase
Ricardo Wurmus skribis:
> I’m happy to be able to submit a patch to add TopHat. It’s a very
> popular piece of bioinformatics software that I didn’t submit to Guix
> upstream before as the license wasn’t clear. The latest release at that
> time contained a LICENSE file with the text of the Arti
Pjotr Prins skribis:
> On Thu, Jan 21, 2016 at 09:55:32PM +0100, Ludovic Courtès wrote:
>> > I wonder how this could be implemented, any ideas?
>>
>> Roughly, we could generate a Scheme file containing the list of phases
>> (the generated build script contains them, but it immediately passes
>>
On Fri, Jan 22, 2016 at 06:58:40PM +0800, 宋文武 wrote:
> Hi, I have push a commit to fix the version script of mozjs, it should
> install correctly now.
>
Thanks, that seems like the right way!
On Fri, Jan 22, 2016 at 05:04:50PM +0100, Pjotr Prins wrote:
> Anyone care to push this?
> On Thu, Jan 21, 2016 at 08:38:48AM +0100, Pjotr Prins wrote:
> > * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4
It has been pushed already, commit 897092875e981678d3c121df3e3d970e90e7eb64
in mas
Anyone care to push this?
On Thu, Jan 21, 2016 at 08:38:48AM +0100, Pjotr Prins wrote:
> * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4
> ---
> gnu/packages/bioinformatics.scm | 4 ++--
> 1 file changed, 2 insertions(+), 2 deletions(-)
>
> diff --git a/gnu/packages/bioinformatics.sc
Andy Wingo writes:
> On Thu 21 Jan 2016 22:25, l...@gnu.org (Ludovic Courtès) writes:
>
>> +2.0.11-3.deadbeef
>
> I thought you were vegetarian :) 2.0.11-3.cabba9e has 7 digits.
>
> Andy, clearly providing very key and crucial feedback
This vegetarian approves of this crucial change :)
~~ Ric
Thanks in advance as usual.
>From 448c2435e50d9d860f1153934058effa42fc6495 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft
Date: Sat, 16 Jan 2016 13:33:08 +1000
Subject: [PATCH] gnu: Add sortmerna.
* gnu/packages/bioinformatics.scm (sortmerna): New variable.
---
gnu/packages/bioinformatics.scm | 3
On 19/01/16 23:52, Ricardo Wurmus wrote:
Hi Guix,
I’m happy to be able to submit a patch to add TopHat. It’s a very
popular piece of bioinformatics software that I didn’t submit to Guix
upstream before as the license wasn’t clear. The latest release at that
time contained a LICENSE file with
Leo Famulari writes:
> * gnu/packages/polkit.scm (polkit)[arguments]: Add LIBJS_LIBS and
> LIBJS_CFLAGS for mozjs-17.
> ---
> gnu/packages/polkit.scm | 14 +++---
> 1 file changed, 11 insertions(+), 3 deletions(-)
>
> diff --git a/gnu/packages/polkit.scm b/gnu/packages/polkit.scm
> index
Hi Ricardo,
I notice that 2.5.1a is now released - I guess you started working on
the patch before it was so.
STARlong is in the binaries that are distributed ie
https://github.com/alexdobin/STAR/tree/master/bin/Linux_x86_64
but this is not built by us since the default make target in source/
On Thu 21 Jan 2016 22:25, l...@gnu.org (Ludovic Courtès) writes:
> +2.0.11-3.deadbeef
I thought you were vegetarian :) 2.0.11-3.cabba9e has 7 digits.
Andy, clearly providing very key and crucial feedback
Roel Janssen skribis:
> Ludovic Courtès writes:
>
>> Roel Janssen skribis:
[...]
>>> Yes, I think it only works when the origin is hydra.gnu.org. I
>>> contacted the sysadmins again to figure this out. Could you leave the
>>> page there for a couple of days? That way I can give them a live
lkit couldn't find mozjs and wouldn't build on core-updates. Maybe due
to the addition of mozjs-24, which I believe happened after the last
release.
I specified the dependency on mozjs-17. It seems that polkit does not
support mozjs-24:
http://lists.freedesktop.org/archives/polkit-devel/2015-July/
* gnu/packages/polkit.scm (polkit)[arguments]: Add LIBJS_LIBS and
LIBJS_CFLAGS for mozjs-17.
---
gnu/packages/polkit.scm | 14 +++---
1 file changed, 11 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/polkit.scm b/gnu/packages/polkit.scm
index 4cafb45..3a119c2 100644
--- a/gnu/pac
* emacs/guix-main.scm (license-names, license-name->license)
(license-name->uri): New procedures.
* emacs/guix-read.el (guix-license-names, guix-read-license-name): New
procedures.
* emacs/guix-license.el: New file.
* emacs.am (ELFILES): Add it.
---
emacs.am | 3 ++-
emacs/guix-l
* emacs/guix-list.el (guix-list-url): New face.
(guix-list-get-url): New procedure.
---
emacs/guix-list.el | 13 +
1 file changed, 13 insertions(+)
diff --git a/emacs/guix-list.el b/emacs/guix-list.el
index 51eb106..c91c67c 100644
--- a/emacs/guix-list.el
+++ b/emacs/guix-list.el
@@
Hello, this patchset adds the following emacs commands:
- guix-browse-license-url
- guix-packages-by-license
- guix-licenses
Patches:
[PATCH 1/7] emacs: Rename 'file-path' to 'file-name'.
Actually this patch is independent from the rest patchset, I just
added it for the company.
[PATCH 2/7
* emacs/guix-main.scm (packages-by-license): New procedure.
(%patterns-makers): Add 'license' search type.
* emacs/guix-messages.el (guix-message-packages-by-license): New procedure.
(guix-messages): Use it.
* emacs/guix-ui-package.el (guix-packages-by-license): New command.
* doc/emacs.texi (Emacs
* emacs/guix-main.scm (%license-param-alist): New variable.
(license->sexp, find-licenses, license-entries): New procedures.
* emacs/guix-license.el (guix-license-get-entries)
(guix-license-get-display, guix-license-insert-packages-button)
(guix-license-insert-comment, guix-license-list-descr
* emacs/guix-ui-package.el (guix-package-license): New button type.
(guix-package-info-format, guix-output-info-format): Use it.
* doc/emacs.texi (Emacs Info buffer): Mention it.
---
doc/emacs.texi | 1 +
emacs/guix-ui-package.el | 12 ++--
2 files changed, 11 insertions(+), 2
* guix/licenses.scm (%licenses): New variable.
---
guix/licenses.scm | 44
1 file changed, 44 insertions(+)
diff --git a/guix/licenses.scm b/guix/licenses.scm
index 9ace7f5..75e4426 100644
--- a/guix/licenses.scm
+++ b/guix/licenses.scm
@@ -2,6 +2,7 @@
* emacs/guix-info.el (guix-info-file-path): Rename to...
(guix-info-file-name): ... this.
* emacs/guix-list.el (guix-list-file-path): Rename to...
(guix-list-file-name): ... this.
(guix-list-get-file-path): Rename to...
(guix-list-get-file-name): ... this.
* emacs/guix-ui-generation.el (gui
49 matches
Mail list logo
