From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: [PATCH] Add SortMeRNA. Date: Sat, 23 Jan 2016 07:55:37 +1000 Message-ID: <56A2A559.6010702@uq.edu.au> References: <56A21CC6.3010906@uq.edu.au> <20160122203556.GA27665@jasmine> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------040603010109090403010908" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:45999) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aMjgO-0002My-PV for guix-devel@gnu.org; Fri, 22 Jan 2016 16:55:54 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aMjgK-00010E-Js for guix-devel@gnu.org; Fri, 22 Jan 2016 16:55:52 -0500 Received: from mailhub2.soe.uq.edu.au ([130.102.132.209]:38624 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aMjgK-0000zO-1S for guix-devel@gnu.org; Fri, 22 Jan 2016 16:55:48 -0500 In-Reply-To: <20160122203556.GA27665@jasmine> 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: Leo Famulari Cc: "guix-devel@gnu.org" This is a multi-part message in MIME format. --------------040603010109090403010908 Content-Type: multipart/alternative; boundary="------------010303080809020303070404" --------------010303080809020303070404 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 7bit 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? > On Fri, Jan 22, 2016 at 10:12:54PM +1000, Ben Woodcroft wrote: [..] >> +(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)? I don't think so. I'm just trusting the tab key and other packages around. No? >> + (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? OK, I've explained it in the description. >> + (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. ben --------------010303080809020303070404 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by newmailhub.uq.edu.au id u0MLteLu010426
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? 
On Fri, Jan 22, 2016 at 10:12:54PM +1000, Ben Woodcr=
oft wrote:
[..]
+(define-public sortmerna
+  (package
+    (name "sortmerna")
+    (version "2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/biocore/sortmerna/arch=
ive/"
+             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
>=20 > 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?

>> +=A0=A0=A0=A0=A0=A0=A0=A0= (replace 'install +=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 (lambda* (#:key output= s >> #:allow-other-keys) +=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 (let* = ((out=A0=A0 (assoc-ref outputs >> "out")) +=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= (bin=A0=A0 (string-append out "/bin")) + >> (share (string-append out "/share/sortmerna/rRNA_databases"))) + >> (install-file "sortmerna" bin) +=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 (install-file >> "indexdb_rna" bin) +=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 (= for-each (lambda (file) + >> (install-file file share)) +=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 (find-files >> "rRNA_databases" ".*fasta")) +=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 #t)))))) + >> (home-page "http://bioinfo.lifl.fr/RNA/sortmerna") += =A0=A0=A0 (synopsis >> "Biological sequence analysis tool for NGS reads") >=20 > Does it make sense to explain the "NGS" acronym anywhere?
OK, I've explained it in the description.

>> +=A0=A0=A0 (description = +=A0=A0=A0=A0 "SortMeRNA is a biological sequence >> analysis tool for filtering, mapping +and operational taxonomic >> unit (OTU) picking next generation sequencing reads. >=20 > 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.


ben

--------------010303080809020303070404-- --------------040603010109090403010908 Content-Type: text/x-patch; name="0001-gnu-Add-sortmerna.patch" Content-Disposition: attachment; filename="0001-gnu-Add-sortmerna.patch" Content-Transfer-Encoding: 7bit >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 --------------040603010109090403010908--