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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: > > 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)?+(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 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 |
0001-gnu-Add-sortmerna.patch
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