From: Mark H Weaver <mhw@netris.org>
To: Ben Woodcroft <b.woodcroft@uq.edu.au>
Cc: guix-devel@gnu.org
Subject: Re: [PATCH] gnu: Add hmmer
Date: Sun, 21 Jun 2015 13:17:31 -0400 [thread overview]
Message-ID: <87egl57zh0.fsf@netris.org> (raw)
In-Reply-To: <55868F4B.6060201@uq.edu.au> (Ben Woodcroft's message of "Sun, 21 Jun 2015 20:17:47 +1000")
Ben Woodcroft <b.woodcroft@uq.edu.au> writes:
> From d49710b5a87bfdbe3c12222fd7f42f4fc67875e5 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <donttrustben@gmail.com>
> Date: Sun, 21 Jun 2015 20:15:31 +1000
> Subject: [PATCH] gnu: Add hmmer.
>
> * gnu/packages/bioinformatics.scm (hmmer): New variable.
> ---
> gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++
> 1 file changed, 24 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 8dfaff3..bb5f942 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -1032,6 +1032,30 @@ 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 license:gpl3+)))
The code in the 'easel' subdirectory is under a different license, "The
Janelia Farm Software License". So you should do something like this:
--8<---------------cut here---------------start------------->8---
(license (list license:gpl3+
;; The bundled library 'easel' is distributed
;; under The Janelia Farm Software License.
(non-copyleft "file://easel/LICENSE"
"See easel/LICENSE in the distribution.")))))
--8<---------------cut here---------------end--------------->8---
It's not good that hmmer bundles its own copy of easel. If we ever need
easel for another package, we should find a way to build hmmer against
the external easel library. Having multiple copies of the same library
on the system potentially means multiple copies in RAM, and more
importantly: multiple copies that need to be patched for fixes,
especially security fixes.
However, we can cross that bridge when we come to it. From a brief
glance, it seems that separating the two will not be trivial :-/
Mark
next prev parent reply other threads:[~2015-06-21 17:17 UTC|newest]
Thread overview: 10+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-06-21 8:52 [PATCH] gnu: Add hmmer Ben Woodcroft
2015-06-21 9:51 ` Ricardo Wurmus
2015-06-21 10:17 ` Ben Woodcroft
2015-06-21 17:17 ` Mark H Weaver [this message]
2015-06-21 18:11 ` Pjotr Prins
2015-06-21 18:23 ` Ricardo Wurmus
2015-06-24 1:37 ` Ben Woodcroft
2015-06-24 1:48 ` Ben Woodcroft
2015-06-24 1:52 ` Ben Woodcroft
2015-06-24 4:41 ` Mark H Weaver
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