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Re: [PATCH] Add SortMeRNA.
From: |
Leo Famulari |
Subject: |
Re: [PATCH] Add SortMeRNA. |
Date: |
Fri, 22 Jan 2016 15:35:56 -0500 |
User-agent: |
Mutt/1.5.24 (2015-08-30) |
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 <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 | 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
>