Re: [PATCH] Add fxtract.

[Ben Woodcroft <b.woodcroft@uq.edu.au>]

On 12/01/16 07:00, Ludovic Courtès wrote:
> Ben Woodcroft <b.woodcroft@uq.edu.au> skribis:
>
>>  From acd310d27c457139d3f2fcd2cfc1127167bf2c48 Mon Sep 17 00:00:00 2001
>> From: Ben Woodcroft <donttrustben@gmail.com>
>> Date: Thu, 7 Jan 2016 07:44:58 +1000
>> Subject: [PATCH] gnu: Add fxtract.
>>
>> * gnu/packages/bioinformatics.scm (fxtract): New variable.
> [...]
>
>> +       `(("ctskennerton-util"
>> +          ,(origin
>> +             (method git-fetch)
>> +             (uri (git-reference
>> +                   (url "https://github.com/ctSkennerton/util.git")
>> +                   (commit util-commit)))
> This is GPLv2-only.  Could you mention it in a comment?
>
>> +             (file-name (string-append
>> +                         "ctstennerton-util-" util-commit "-checkout"))
> I would make it:
>
>    (string-append "ctstennerton-util-" (string-take util-commit 7)
>                   "-checkout")
>
>> +      (home-page "https://github.com/ctSkennerton/fxtract")
>> +      (synopsis "Extract sequences from FASTA and FASTQ files")
>> +      (description
>> +       "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA
>> +or FASTQ) file given a subsequence.  It uses a simple substring search for
>> +basic tasks but can change to using POSIX regular expressions, PCRE, hash
>> +lookups or multi-pattern searching as required.  By default fxtract looks in
>> +the sequence of each record but can also be told to look in the header,
>> +comment or quality sections.")
>> +      (license license:gpl3+))))
> According to the ‘LICENSE’ file, this should be ‘license:expat’.
>
> Otherwise LGTM.

Pushed with these changes. Thanks for picking up the mistakes.

ben