Re: [PATCH] gnu: Add hmmer

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

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Thanks Mark, that's the only change in the attached patch, except that 
"license:" is added too.

On 22/06/15 04:23, Ricardo Wurmus wrote:
> Pjotr Prins <pjotr.public12@thebird.nl> writes:
>
>> It is quite common in bioinformatics tools to include foreign code.
>> One reason in favour of including the original setup that is it is
>> THAT what the authors and others test and run. Bringing in our own
>> dependencies is bound to open a can of worms - there often is a reason
>> they bring in that packaged code. One reason is that they depend on an older
>> version ;).
> With Guix we have no problem with packaging older versions.  I have
> untangled a number of applications with bundled libraries before.  It is
> doable, better for reproducibility, and better for security.
>
> I often submit bug reports upstream when I encounter bundling when
> attempting to package software and I encourage others to do the same.
>
> ~~ Ricardo
In general I agree Ricardo. I find devs do this sometimes also because 
they are trying to help their users. It is as if they need some kind of 
package distribution system. Hopefully if guix takes off devs will 
increasingly not bundle dependencies because they can rely on guix to do 
it for them, in turn making them easier to package. In this case easel 
is quite baked in from my brief look e.g. hard coded paths to it in 
configure.ac, and anyway I was unable to source easel separately (the 
bioeasel.org domain seems to have lapsed), and I'm not aware of many 
other software packages using it anyway (but cannot know for sure).

Speaking of pleasant thoughts, for many reasons there's a lot of 
software in bioinformatics that has zero testing, which is bad. The 
pleasant thing is that in a packaging system that runs tests of packages 
that rely on other packages, if the downstream package has tests that 
fail because the upstream package no longer works then hydra will know 
about this through the magic of continuous integrations. So I don't need 
to write tests for my software, I just need to make sure the software is 
used by other devs that do use tests, right?

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From 5002a93221dbd77c8dbb4212eb463e13bf4b9361 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Wed, 24 Jun 2015 11:16:53 +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..32d1cbd 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