>From 12e455874cf563269efc872235738e0ab4848638 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <address@hidden>
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