From: Ben Woodcroft <donttrustben@gmail.com>
To: guix-devel@gnu.org
Subject: [PATCH] gnu: Add seqtk.
Date: Fri, 9 Sep 2016 21:08:34 +1000 [thread overview]
Message-ID: <20160909110834.8581-1-donttrustben@gmail.com> (raw)
In-Reply-To: <20150718090748.GA26418@jocasta.intra>
From: Ben J Woodcroft <donttrustben@gmail.com>
Well, despite the lightness of my touch, it seems the licensing is in now in
order. I've updated the package, here's an updated patch. Better?
Thanks,
ben
* gnu/packages/bioinformatics.scm (seqtk): New variable.
---
gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f34acd1..4e296f5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4529,6 +4529,41 @@ BioPython in a convenient way. Instead of having a big mess of scripts, there
is one that takes arguments.")
(license license:gpl3)))
+(define-public seqtk
+ (package
+ (name "seqtk")
+ (version "1.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/lh3/seqtk/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'check
+ ;; There are no tests, so we just run a sanity check.
+ (lambda _ (zero? (system* "./seqtk" "seq"))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (install-file "seqtk" bin)))))))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://github.com/lh3/seqtk")
+ (synopsis "Toolkit for biological sequences in FASTA/Q formats")
+ (description
+ "Seqtk is a fast and lightweight tool for processing sequences in the
+FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be
+optionally compressed by gzip.")
+ (license license:expat)))
+
(define-public snap-aligner
(package
(name "snap-aligner")
--
2.9.1
next prev parent reply other threads:[~2016-09-09 11:08 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-06-24 5:07 [PATCH] Add seqtk Ben Woodcroft
2015-06-24 12:09 ` Mark H Weaver
2015-07-18 7:51 ` Ben Woodcroft
2015-07-18 9:07 ` John Darrington
2016-09-09 11:08 ` Ben Woodcroft [this message]
2016-09-09 12:37 ` [PATCH] gnu: " Marius Bakke
2016-09-09 12:54 ` Marius Bakke
2016-09-10 4:03 ` Ben Woodcroft
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