Re: [PATCH] Add SortMeRNA.

[Leo Famulari <leo@famulari.name>]

On Fri, Jan 22, 2016 at 10:12:54PM +1000, Ben Woodcroft wrote:
> Thanks in advance as usual.

> From 448c2435e50d9d860f1153934058effa42fc6495 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <donttrustben@gmail.com>
> Date: Sat, 16 Jan 2016 13:33:08 +1000
> Subject: [PATCH] gnu: Add sortmerna.
> 
> * gnu/packages/bioinformatics.scm (sortmerna): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++
>  1 file changed, 39 insertions(+)
> 
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index e579afe..e170ff7 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -3016,6 +3016,45 @@ optimized for modern read lengths of 100 bases or higher, and takes advantage
>  of these reads to align data quickly through a hash-based indexing scheme.")
>      (license license:asl2.0)))
>  
> +(define-public sortmerna
> +  (package
> +    (name "sortmerna")
> +    (version "2.0")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (string-append
> +             "https://github.com/biocore/sortmerna/archive/"
> +             version ".tar.gz"))
> +       (file-name (string-append name "-" version ".tar.gz"))
> +       (sha256
> +        (base32
> +         "1670a92x1vvkacnvgr2i5xac3ls6lp4pc3n0bccnmllsnymggcf0"))))
> +    (build-system gnu-build-system)
> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases

My sense of Scheme style is still pretty weak but shouldn't the above
line move one character to the right (along with the remainder of
arguments)?

> +         (replace 'install
> +           (lambda* (#:key outputs #:allow-other-keys)
> +             (let* ((out   (assoc-ref outputs "out"))
> +                    (bin   (string-append out "/bin"))
> +                    (share (string-append out "/share/sortmerna/rRNA_databases")))
> +               (install-file "sortmerna" bin)
> +               (install-file "indexdb_rna" bin)
> +               (for-each (lambda (file)
> +                           (install-file file share))
> +                         (find-files "rRNA_databases" ".*fasta"))
> +               #t))))))
> +    (home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
> +    (synopsis "Biological sequence analysis tool for NGS reads")

Does it make sense to explain the "NGS" acronym anywhere?

> +    (description
> +     "SortMeRNA is a biological sequence analysis tool for filtering, mapping
> +and operational taxonomic unit (OTU) picking next generation sequencing reads.

Does this sentence make more sense with "of" inserted between "picking"
and "next"?

> +The core algorithm is based on approximate seeds and allows for fast and
> +sensitive analyses of nucleotide sequences.  The main application of SortMeRNA
> +is filtering rRNA from metatranscriptomic data.")
> +    (license license:lgpl3)))
> +
>  (define-public star
>    (package
>      (name "star")
> -- 
> 2.6.3
>