* [PATCH] Add aragorn.
@ 2015-07-21 13:14 Ben Woodcroft
2015-07-21 13:40 ` Ricardo Wurmus
0 siblings, 1 reply; 6+ messages in thread
From: Ben Woodcroft @ 2015-07-21 13:14 UTC (permalink / raw)
To: guix-devel@gnu.org
[-- Attachment #1: Type: text/plain, Size: 1 bytes --]
[-- Attachment #2: 0001-gnu-Add-aragorn.patch --]
[-- Type: text/x-patch, Size: 2910 bytes --]
From 12e455874cf563269efc872235738e0ab4848638 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Tue, 21 Jul 2015 23:08:58 +1000
Subject: [PATCH] gnu: Add aragorn.
* gnu/packages/bioinformatics.scm (aragorn): New variable
---
gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 51 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 78cd3ce..1d226ca 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -54,6 +54,57 @@
#:use-module (gnu packages xml)
#:use-module (gnu packages zip))
+(define-public aragorn
+ (package
+ (name "aragorn")
+ (version "1.2.36")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn"
+ version ".tgz"))
+ (file-name (string-append name "-" version ".tgz"))
+ (sha256
+ (base32
+ "1dg7jlz1qpqy88igjxd6ncs11ccsirb36qv1z01a0np4i4jh61mb"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are no tests
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'build
+ (lambda _
+ (zero? (system* "gcc"
+ "-O3"
+ "-ffast-math"
+ "-finline-functions"
+ "-o"
+ "aragorn"
+ (string-append
+ "aragorn" ,version ".c")))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append
+ (assoc-ref outputs "out") "/bin"))
+ (man (string-append
+ (assoc-ref outputs "out") "/share/man/man1")))
+ (mkdir-p bin)
+ (copy-file "aragorn"
+ (string-append bin "/aragorn"))
+ (mkdir-p man)
+ (copy-file "aragorn.1"
+ (string-append man "/aragorn.1")))
+ #t)))))
+ (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN")
+ (synopsis
+ "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
+ (description
+ "Aragorn identifies transfer RNA and transfer-messenger RNA sequences from
+nucleotide sequences, based on homology to known tRNA consensus sequences and
+RNA structure. It output the secondary structure of the predicted RNA.")
+ (license license:gpl2)))
+
(define-public bamtools
(package
(name "bamtools")
--
2.4.3
^ permalink raw reply related [flat|nested] 6+ messages in thread
* Re: [PATCH] Add aragorn.
2015-07-21 13:14 [PATCH] Add aragorn Ben Woodcroft
@ 2015-07-21 13:40 ` Ricardo Wurmus
2015-07-21 13:55 ` Ben Woodcroft
0 siblings, 1 reply; 6+ messages in thread
From: Ricardo Wurmus @ 2015-07-21 13:40 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: guix-devel@gnu.org
Ben Woodcroft <b.woodcroft@uq.edu.au> writes:
> +(define-public aragorn
> + (package
> + (name "aragorn")
> + (version "1.2.36")
> + (source (origin
> + (method url-fetch)
> + (uri (string-append
> + "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn"
> + version ".tgz"))
> + (file-name (string-append name "-" version ".tgz"))
Is this really necessary? The version is included in the tarball name,
it just doesn’t look like “name-version.tgz” but like
“nameversion.tgz”. I think it could be left off.
> + (sha256
> + (base32
> + "1dg7jlz1qpqy88igjxd6ncs11ccsirb36qv1z01a0np4i4jh61mb"))))
> + (build-system gnu-build-system)
> + (arguments
> + `(#:tests? #f ; there are no tests
> + #:phases
> + (modify-phases %standard-phases
> + (delete 'configure)
> + (replace 'build
> + (lambda _
> + (zero? (system* "gcc"
> + "-O3"
> + "-ffast-math"
> + "-finline-functions"
> + "-o"
> + "aragorn"
> + (string-append
> + "aragorn" ,version ".c")))))
> + (replace 'install
> + (lambda* (#:key outputs #:allow-other-keys)
> + (let ((bin (string-append
> + (assoc-ref outputs "out") "/bin"))
> + (man (string-append
> + (assoc-ref outputs "out") "/share/man/man1")))
> + (mkdir-p bin)
> + (copy-file "aragorn"
> + (string-append bin "/aragorn"))
> + (mkdir-p man)
> + (copy-file "aragorn.1"
> + (string-append man "/aragorn.1")))
> + #t)))))
> + (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN")
> + (synopsis
> + "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
> + (description
> + "Aragorn identifies transfer RNA and transfer-messenger RNA sequences from
> +nucleotide sequences, based on homology to known tRNA consensus sequences and
> +RNA structure. It output the secondary structure of the predicted RNA.")
There is a space missing at the end of the sentence. Double-spacing
should be used.
> + (license license:gpl2)))
> +
Other than that it looks fine to me! Thanks!
~~ Ricardo
^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [PATCH] Add aragorn.
2015-07-21 13:40 ` Ricardo Wurmus
@ 2015-07-21 13:55 ` Ben Woodcroft
2015-07-21 13:57 ` Ricardo Wurmus
0 siblings, 1 reply; 6+ messages in thread
From: Ben Woodcroft @ 2015-07-21 13:55 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel@gnu.org
[-- Attachment #1: Type: text/plain, Size: 153 bytes --]
On 21/07/15 23:40, Ricardo Wurmus wrote:
> Other than that it looks fine to me! Thanks!
Ta. Fixed those two things plus some grammar in the description.
[-- Attachment #2: 0001-gnu-Add-aragorn.patch --]
[-- Type: text/x-patch, Size: 2860 bytes --]
From 4ac97beef55a5321a9990244ebfcdde38051ff9a Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Tue, 21 Jul 2015 23:52:31 +1000
Subject: [PATCH] gnu: Add aragorn.
* gnu/packages/bioinformatics.scm (aragorn): New variable
---
gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 51 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 78cd3ce..8028b49 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -54,6 +54,57 @@
#:use-module (gnu packages xml)
#:use-module (gnu packages zip))
+(define-public aragorn
+ (package
+ (name "aragorn")
+ (version "1.2.36")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn"
+ version ".tgz"))
+ (sha256
+ (base32
+ "1dg7jlz1qpqy88igjxd6ncs11ccsirb36qv1z01a0np4i4jh61mb"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are no tests
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'build
+ (lambda _
+ (zero? (system* "gcc"
+ "-O3"
+ "-ffast-math"
+ "-finline-functions"
+ "-o"
+ "aragorn"
+ (string-append
+ "aragorn" ,version ".c")))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append
+ (assoc-ref outputs "out") "/bin"))
+ (man (string-append
+ (assoc-ref outputs "out") "/share/man/man1")))
+ (mkdir-p bin)
+ (copy-file "aragorn"
+ (string-append bin "/aragorn"))
+ (mkdir-p man)
+ (copy-file "aragorn.1"
+ (string-append man "/aragorn.1")))
+ #t)))))
+ (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN")
+ (synopsis
+ "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
+ (description
+ "Aragorn identifies transfer RNA, mitochondrial RNA and
+transfer-messenger RNA from nucleotide sequences, based on homology to known
+tRNA consensus sequences and RNA structure. It also outputs the secondary
+structure of the predicted RNA.")
+ (license license:gpl2)))
+
(define-public bamtools
(package
(name "bamtools")
--
2.4.3
^ permalink raw reply related [flat|nested] 6+ messages in thread
* Re: [PATCH] Add aragorn.
2015-07-21 13:55 ` Ben Woodcroft
@ 2015-07-21 13:57 ` Ricardo Wurmus
2015-07-21 14:01 ` Thompson, David
0 siblings, 1 reply; 6+ messages in thread
From: Ricardo Wurmus @ 2015-07-21 13:57 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: guix-devel@gnu.org
Something’s wrong with the alignment of the ‘(replace 'install ...)’.
If there are no objections I can fix the alignment and push without
requesting another version of the patch.
But I think I better wait for other comments.
^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [PATCH] Add aragorn.
2015-07-21 13:57 ` Ricardo Wurmus
@ 2015-07-21 14:01 ` Thompson, David
2015-07-21 14:42 ` Ricardo Wurmus
0 siblings, 1 reply; 6+ messages in thread
From: Thompson, David @ 2015-07-21 14:01 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel@gnu.org
On Tue, Jul 21, 2015 at 9:57 AM, Ricardo Wurmus
<ricardo.wurmus@mdc-berlin.de> wrote:
> Something’s wrong with the alignment of the ‘(replace 'install ...)’.
> If there are no objections I can fix the alignment and push without
> requesting another version of the patch.
>
> But I think I better wait for other comments.
Looks fine to me, sans the alignment. One additional nitpick is the
'string-append' calls. The newlines should happen *after* the first
argument, not before.
- Dave
^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [PATCH] Add aragorn.
2015-07-21 14:01 ` Thompson, David
@ 2015-07-21 14:42 ` Ricardo Wurmus
0 siblings, 0 replies; 6+ messages in thread
From: Ricardo Wurmus @ 2015-07-21 14:42 UTC (permalink / raw)
To: Thompson, David; +Cc: guix-devel@gnu.org
Thompson, David <dthompson2@worcester.edu> writes:
> On Tue, Jul 21, 2015 at 9:57 AM, Ricardo Wurmus
> <ricardo.wurmus@mdc-berlin.de> wrote:
>> Something’s wrong with the alignment of the ‘(replace 'install ...)’.
>> If there are no objections I can fix the alignment and push without
>> requesting another version of the patch.
>>
>> But I think I better wait for other comments.
>
> Looks fine to me, sans the alignment. One additional nitpick is the
> 'string-append' calls. The newlines should happen *after* the first
> argument, not before.
I fixed the alignment and made a couple of small modifications to
prettify the ‘string-append’ calls. Pushed as 8dc797f.
Thanks again!
~~ Ricardo
^ permalink raw reply [flat|nested] 6+ messages in thread
end of thread, other threads:[~2015-07-21 14:42 UTC | newest]
Thread overview: 6+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2015-07-21 13:14 [PATCH] Add aragorn Ben Woodcroft
2015-07-21 13:40 ` Ricardo Wurmus
2015-07-21 13:55 ` Ben Woodcroft
2015-07-21 13:57 ` Ricardo Wurmus
2015-07-21 14:01 ` Thompson, David
2015-07-21 14:42 ` Ricardo Wurmus
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/guix.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).