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* [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

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[-- Attachment #2: 0001-gnu-Add-aragorn.patch --]
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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

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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.

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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

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