Re: [PATCH] Add SortMeRNA.

[Leo Famulari]

On Sat, Jan 23, 2016 at 07:55:37AM +1000, Ben Woodcroft wrote:
> 
> On 23/01/16 06:35, Leo Famulari wrote:
> >On Fri, Jan 22, 2016 at 10:12:54PM +1000, Ben Woodcroft wrote:
> [..]
> 
> Thanks Leo. As well as responding to your review the attached patch breaks
> out the rRNA databases out into a separate output "db", removing 73MB from
> the default package. Is "db" a good name?

Sounds like a good name. It's a good idea to split the package up if the
database is not necessary for a basic installation. I haven't used
multiple outputs in my packages yet so I can't say if your
implementation is correct or not.

> >On Fri, Jan 22, 2016 at 10:12:54PM +1000, Ben Woodcroft wrote:
> [..]
> >>+    (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)?
> I don't think so. I'm just trusting the tab key and other packages around.
> No?

Like I said, my sense of style is not very developed ;) I checked some
other packages and they agree with you.

> >>+    (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"?
> I think either way is fine, but including the of rolls of the tongue a bit
> better.

The original was a garden path sentence to my ears. However, I am
reading the sentence as a layperson so the meaning is mostly lost on me.

> 
> 
> ben
> 

> From 6f2599eff86b5a67a92429756f2df3ba2cf53201 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <address@hidden>
> 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 | 43 
> +++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 43 insertions(+)
> 
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index e579afe..946083f 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -3016,6 +3016,49 @@ 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)
> +    (outputs '("out"      ;for binaries
> +               "db"))     ;for sequence databases
> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         (replace 'install
> +           (lambda* (#:key outputs #:allow-other-keys)
> +             (let* ((out   (assoc-ref outputs "out"))
> +                    (bin   (string-append out "/bin"))
> +                    (db    (assoc-ref outputs "db"))
> +                    (share
> +                     (string-append db "/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")
> +    (description
> +     "SortMeRNA is a biological sequence analysis tool for filtering, mapping
> +and operational taxonomic unit (OTU) picking of next generation
> +sequencing (NGS) reads.  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
>