* [PATCH] Add fxtract.
@ 2016-01-06 21:48 Ben Woodcroft
2016-01-11 21:00 ` Ludovic Courtès
0 siblings, 1 reply; 3+ messages in thread
From: Ben Woodcroft @ 2016-01-06 21:48 UTC (permalink / raw)
To: guix-devel@gnu.org
[-- Attachment #1: Type: text/plain, Size: 34 bytes --]
Thanks in advance for review.
ben
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-gnu-Add-fxtract.patch --]
[-- Type: text/x-patch; name="0001-gnu-Add-fxtract.patch", Size: 4155 bytes --]
From acd310d27c457139d3f2fcd2cfc1127167bf2c48 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 7 Jan 2016 07:44:58 +1000
Subject: [PATCH] gnu: Add fxtract.
* gnu/packages/bioinformatics.scm (fxtract): New variable.
---
gnu/packages/bioinformatics.scm | 65 ++++++++++++++++++++++++++++++++++++++++-
1 file changed, 64 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 76a1c17..77fe411 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;;
@@ -47,6 +47,7 @@
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages ncurses)
+ #:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
@@ -1436,6 +1437,68 @@ genes in incomplete assemblies or complete genomes.")
;; GPL3+ according to private correspondense with the authors.
(license license:gpl3+)))
+(define-public fxtract
+ (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115"))
+ (package
+ (name "fxtract")
+ (version "2.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ctSkennerton/fxtract/archive/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:make-flags (list
+ (string-append "PREFIX=" (assoc-ref %outputs "out"))
+ "CC=gcc")
+ #:test-target "fxtract_test"
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'build 'copy-util
+ (lambda* (#:key inputs #:allow-other-keys)
+ (rmdir "util")
+ (copy-recursively (assoc-ref inputs "ctskennerton-util") "util")
+ #t))
+ ;; Do not use make install as this requires additional dependencies.
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out"/bin")))
+ (install-file "fxtract" bin)
+ #t))))))
+ (inputs
+ `(("pcre" ,pcre)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("ctskennerton-util"
+ ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ctSkennerton/util.git")
+ (commit util-commit)))
+ (file-name (string-append
+ "ctstennerton-util-" util-commit "-checkout"))
+ (sha256
+ (base32
+ "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7"))))))
+ (home-page "https://github.com/ctSkennerton/fxtract")
+ (synopsis "Extract sequences from FASTA and FASTQ files")
+ (description
+ "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA
+or FASTQ) file given a subsequence. It uses a simple substring search for
+basic tasks but can change to using POSIX regular expressions, PCRE, hash
+lookups or multi-pattern searching as required. By default fxtract looks in
+the sequence of each record but can also be told to look in the header,
+comment or quality sections.")
+ (license license:gpl3+))))
+
(define-public grit
(package
(name "grit")
--
2.6.3
^ permalink raw reply related [flat|nested] 3+ messages in thread
* Re: [PATCH] Add fxtract.
2016-01-06 21:48 [PATCH] Add fxtract Ben Woodcroft
@ 2016-01-11 21:00 ` Ludovic Courtès
2016-01-11 21:53 ` Ben Woodcroft
0 siblings, 1 reply; 3+ messages in thread
From: Ludovic Courtès @ 2016-01-11 21:00 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: guix-devel@gnu.org
Ben Woodcroft <b.woodcroft@uq.edu.au> skribis:
> From acd310d27c457139d3f2fcd2cfc1127167bf2c48 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <donttrustben@gmail.com>
> Date: Thu, 7 Jan 2016 07:44:58 +1000
> Subject: [PATCH] gnu: Add fxtract.
>
> * gnu/packages/bioinformatics.scm (fxtract): New variable.
[...]
> + `(("ctskennerton-util"
> + ,(origin
> + (method git-fetch)
> + (uri (git-reference
> + (url "https://github.com/ctSkennerton/util.git")
> + (commit util-commit)))
This is GPLv2-only. Could you mention it in a comment?
> + (file-name (string-append
> + "ctstennerton-util-" util-commit "-checkout"))
I would make it:
(string-append "ctstennerton-util-" (string-take util-commit 7)
"-checkout")
> + (home-page "https://github.com/ctSkennerton/fxtract")
> + (synopsis "Extract sequences from FASTA and FASTQ files")
> + (description
> + "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA
> +or FASTQ) file given a subsequence. It uses a simple substring search for
> +basic tasks but can change to using POSIX regular expressions, PCRE, hash
> +lookups or multi-pattern searching as required. By default fxtract looks in
> +the sequence of each record but can also be told to look in the header,
> +comment or quality sections.")
> + (license license:gpl3+))))
According to the ‘LICENSE’ file, this should be ‘license:expat’.
Otherwise LGTM.
Thanks,
Ludo’.
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: [PATCH] Add fxtract.
2016-01-11 21:00 ` Ludovic Courtès
@ 2016-01-11 21:53 ` Ben Woodcroft
0 siblings, 0 replies; 3+ messages in thread
From: Ben Woodcroft @ 2016-01-11 21:53 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: guix-devel@gnu.org, Connor Skennerton
On 12/01/16 07:00, Ludovic Courtès wrote:
> Ben Woodcroft <b.woodcroft@uq.edu.au> skribis:
>
>> From acd310d27c457139d3f2fcd2cfc1127167bf2c48 Mon Sep 17 00:00:00 2001
>> From: Ben Woodcroft <donttrustben@gmail.com>
>> Date: Thu, 7 Jan 2016 07:44:58 +1000
>> Subject: [PATCH] gnu: Add fxtract.
>>
>> * gnu/packages/bioinformatics.scm (fxtract): New variable.
> [...]
>
>> + `(("ctskennerton-util"
>> + ,(origin
>> + (method git-fetch)
>> + (uri (git-reference
>> + (url "https://github.com/ctSkennerton/util.git")
>> + (commit util-commit)))
> This is GPLv2-only. Could you mention it in a comment?
>
>> + (file-name (string-append
>> + "ctstennerton-util-" util-commit "-checkout"))
> I would make it:
>
> (string-append "ctstennerton-util-" (string-take util-commit 7)
> "-checkout")
>
>> + (home-page "https://github.com/ctSkennerton/fxtract")
>> + (synopsis "Extract sequences from FASTA and FASTQ files")
>> + (description
>> + "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA
>> +or FASTQ) file given a subsequence. It uses a simple substring search for
>> +basic tasks but can change to using POSIX regular expressions, PCRE, hash
>> +lookups or multi-pattern searching as required. By default fxtract looks in
>> +the sequence of each record but can also be told to look in the header,
>> +comment or quality sections.")
>> + (license license:gpl3+))))
> According to the ‘LICENSE’ file, this should be ‘license:expat’.
>
> Otherwise LGTM.
Pushed with these changes. Thanks for picking up the mistakes.
ben
^ permalink raw reply [flat|nested] 3+ messages in thread
end of thread, other threads:[~2016-01-11 21:53 UTC | newest]
Thread overview: 3+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2016-01-06 21:48 [PATCH] Add fxtract Ben Woodcroft
2016-01-11 21:00 ` Ludovic Courtès
2016-01-11 21:53 ` Ben Woodcroft
Code repositories for project(s) associated with this external index
https://git.savannah.gnu.org/cgit/guix.git
This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.