From: Ben Woodcroft <b.woodcroft@uq.edu.au>
To: "guix-devel@gnu.org" <guix-devel@gnu.org>
Subject: [PATCH] Add aragorn.
Date: Tue, 21 Jul 2015 23:14:01 +1000 [thread overview]
Message-ID: <55AE4599.5040601@uq.edu.au> (raw)
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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
next reply other threads:[~2015-07-21 13:14 UTC|newest]
Thread overview: 6+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-07-21 13:14 Ben Woodcroft [this message]
2015-07-21 13:40 ` [PATCH] Add aragorn 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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