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Re: [PATCH] Add SortMeRNA.


From: Ben Woodcroft
Subject: Re: [PATCH] Add SortMeRNA.
Date: Sat, 23 Jan 2016 07:55:37 +1000
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:38.0) Gecko/20100101 Thunderbird/38.5.1


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

Attachment: 0001-gnu-Add-sortmerna.patch
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