Re: [PATCH] gnu: Add Infernal.

[Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>]

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