Re: [PATCH] gnu: Add hmmer

[Ben Woodcroft <b.woodcroft@uq.edu.au>]

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On 24/06/15 11:48, Ben Woodcroft wrote:
>
> On 24/06/15 11:37, Ben Woodcroft wrote:
>> Thanks Mark, that's the only change in the attached patch, except 
>> that "license:" is added too.
> Actually I didn't, I'll send an updated patch soon after testing.
>
Attached, seems all good now. Apologies for sending too many mails about 
this.

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From 936ad4f76bbb3825ab5c1623285756cf45f8d192 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Wed, 24 Jun 2015 11:51:05 +1000
Subject: [PATCH] gnu: Add hmmer.

* gnu/packages/bioinformatics.scm (hmmer): New variable.
---
 gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8dfaff3..c88c3ab 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1032,6 +1032,35 @@ several alignment strategies enable effective alignment of RNA-seq reads, in
 particular, reads spanning multiple exons.")
     (license license:gpl3+)))
 
+(define-public hmmer
+  (package
+    (name "hmmer")
+    (version "3.1b2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://selab.janelia.org/software/hmmer"
+                    (version-prefix version 1) "/"
+                    version "/hmmer-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))))
+    (build-system gnu-build-system)
+    (native-inputs `(("perl", perl)))
+    (home-page "http://hmmer.janelia.org")
+    (synopsis "Biosequence analysis using profile hidden Markov models")
+    (description
+     "HMMER is used for searching sequence databases for homologs of protein
+sequences, and for making protein sequence alignments.  It implements methods
+using probabilistic models called profile hidden Markov models (profile
+HMMs).")
+    (license (list license:gpl3+
+                   ;; The bundled library 'easel' is distributed
+                   ;; under The Janelia Farm Software License.
+                   (license:non-copyleft
+                    "file://easel/LICENSE"
+                    "See easel/LICENSE in the distribution.")))))
+
 (define-public htseq
   (package
     (name "htseq")
-- 
2.1.4