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
>From 6f2599eff86b5a67a92429756f2df3ba2cf53201 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <[email protected]>
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
