Re: [PATCH] gnu: Add Infernal.

["Thompson, David" <dthompson2@worcester.edu>]

On Fri, Sep 2, 2016 at 9:35 AM, Ricardo Wurmus
<ricardo.wurmus@mdc-berlin.de> wrote:
> * gnu/packages/bioinformatics.scm (infernal): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
>  1 file changed, 27 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 08c2545..1652f71 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -4835,6 +4835,33 @@ data in the form of VCF files.")
>      ;; at https://vcftools.github.io/license.html
>      (license license:lgpl3)))
>
> +(define-public infernal
> +  (package
> +    (name "infernal")
> +    (version "1.1.2")
> +    (source (origin
> +              (method url-fetch)
> +              ;; There are no versioned tarballs

But the version appears in the URL?

> +              (uri (string-append "http://eddylab.org/software/infernal/"
> +                                  "infernal-" version ".tar.gz"))
> +              (sha256
> +               (base32
> +                "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c"))))
> +    (build-system gnu-build-system)
> +    (native-inputs
> +     `(("perl" ,perl))) ; for tests
> +    (home-page "http://eddylab.org/infernal/")
> +    (synopsis "Inference of RNA alignments")
> +    (description "Infernal (\"INFERence of RNA ALignment\") is a tool for
> +searching DNA sequence databases for RNA structure and sequence similarities.
> +It is an implementation of a special case of profile stochastic context-free
> +grammars called @dfn{covariance models} (CMs).  A CM is like a sequence
> +profile, but it scores a combination of sequence consensus and RNA secondary
> +structure consensus, so in many cases, it is more capable of identifying RNA
> +homologs that conserve their secondary structure more than their primary
> +sequence.")
> +    (license license:bsd-3)))
> +
>  (define-public r-vegan
>    (package
>      (name "r-vegan")
> --
> 2.9.3
>
>

LGTM overall.

- Dave