Ben Woodcroft <b.woodcr...@uq.edu.au> writes:
> From d49710b5a87bfdbe3c12222fd7f42f4fc67875e5 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <donttrust...@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
