Re: [PATCH] gnu: Add Infernal.

[Efraim Flashner <efraim@flashner.co.il>]

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On Fri, Sep 02, 2016 at 04:12:21PM +0200, Ricardo Wurmus wrote:
> 
> Thompson, David <dthompson2@worcester.edu> writes:
> 
> > 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?
> 
> 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.

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Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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