Re: [PATCH] Add fxtract.

[ludo@gnu.org (Ludovic Courtès)]

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.

Thanks,
Ludo’.