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