From mboxrd@z Thu Jan 1 00:00:00 1970 From: Leo Famulari Subject: Re: [PATCH] Add SortMeRNA. Date: Fri, 22 Jan 2016 18:00:17 -0500 Message-ID: <20160122230017.GA30057@jasmine> References: <56A21CC6.3010906@uq.edu.au> <20160122203556.GA27665@jasmine> <56A2A559.6010702@uq.edu.au> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:56080) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aMkgn-0004mX-Jx for guix-devel@gnu.org; Fri, 22 Jan 2016 18:00:22 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aMkgi-0005zs-TI for guix-devel@gnu.org; Fri, 22 Jan 2016 18:00:21 -0500 Received: from out3-smtp.messagingengine.com ([66.111.4.27]:36783) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aMkgi-0005zo-OQ for guix-devel@gnu.org; Fri, 22 Jan 2016 18:00:16 -0500 Received: from compute4.internal (compute4.nyi.internal [10.202.2.44]) by mailout.nyi.internal (Postfix) with ESMTP id B06C021947 for ; Fri, 22 Jan 2016 18:00:15 -0500 (EST) Content-Disposition: inline In-Reply-To: <56A2A559.6010702@uq.edu.au> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Ben Woodcroft Cc: "guix-devel@gnu.org" 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 > 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 >