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Re: [PATCH] gnu: Add Infernal.
From: |
Efraim Flashner |
Subject: |
Re: [PATCH] gnu: Add Infernal. |
Date: |
Mon, 5 Sep 2016 12:32:08 +0300 |
User-agent: |
Mutt/1.7.0 (2016-08-17) |
On Fri, Sep 02, 2016 at 04:12:21PM +0200, Ricardo Wurmus wrote:
>
> Thompson, David <address@hidden> writes:
>
> > 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?
>
> Sorry, this comment was supposed to be removed before sending out the
> patch. Noticed it too late.
>
> >> + (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.
>
> Okay, will push in a moment (after removing the wrong comment).
> Thanks for taking a look!
>
> ~~ Ricardo
>
After checking the hydra logs I removed support for armhf and mips,
since they lack the necessary hardware features to build the package.
--
Efraim Flashner <address@hidden> אפרים פלשנר
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