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Re: [PATCH] gnu: Add Infernal.
From: |
Thompson, David |
Subject: |
Re: [PATCH] gnu: Add Infernal. |
Date: |
Fri, 2 Sep 2016 09:44:10 -0400 |
On Fri, Sep 2, 2016 at 9:35 AM, Ricardo Wurmus
<address@hidden> 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