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Re: [PATCH] gnu: Add Infernal.
From: |
Ricardo Wurmus |
Subject: |
Re: [PATCH] gnu: Add Infernal. |
Date: |
Fri, 2 Sep 2016 16:12:21 +0200 |
User-agent: |
mu4e 0.9.16; emacs 24.5.1 |
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