Re: [PATCH] gnu: Add ParDRe.

[Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>]

Roel Janssen <roel@gnu.org> writes:

> Ricardo Wurmus writes:
>
>> * gnu/packages/bioinformatics.scm (pardre): New variable.
>> ---
>>  gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++++++++++
>>  1 file changed, 41 insertions(+)
>>
>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>> index 787f386..e681c56 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -4111,6 +4111,47 @@ Needleman-Wunsch).")
>>      ;; Dual licensed; also includes public domain source.
>>      (license (list license:gpl3 license:bsd-2))))
>>  
>> +(define-public pardre
>> +  (package
>> +    (name "pardre")
>> +    (version "1.1.5")
>> +    (source
>> +     (origin
>> +       (method url-fetch)
>> +       (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel"
>> +                           version ".tar.gz"))
>> +       (sha256
>> +        (base32
>> +         "0zkyjzv4s8q2h5npalhirbk17r5b1h0n2a42mh7njzlf047h9bhy"))))
>> +    (build-system gnu-build-system)
>> +    (arguments
>> +     `(#:tests? #f ; no tests included
>> +       #:phases
>> +       (modify-phases %standard-phases
>> +         (delete 'configure)
>> +         (replace 'install
>> +           (lambda* (#:key outputs #:allow-other-keys)
>> +             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
>> +               (mkdir-p bin)
>> +               (install-file "ParDRe" bin)
>> +               #t))))))
>> +    (inputs
>> +     `(("openmpi" ,openmpi)
>> +       ("zlib" ,zlib)))
>> +    (synopsis "Parallel tool to remove duplicate DNA reads ")
>
> It would be nice to remove the space at the end of the synopsis.

Good catch!

>> +    (description
>> +     "ParDRe is a parallel tool to remove duplicate genetic sequence reads.
>> +Duplicate reads can be seen as identical or nearly identical sequences with
>> +some mismatches.  This tool will let the users to avoid the analysis of not
>> +necessary reads, reducing the time of subsequent procedures with the
>> +dataset (e.g., assemblies, mappings, etc.).  The tool is implemented with MPI
>> +in order to exploit the parallel capabilities of multicore clusters.  It is
>> +faster than multithreaded counterparts (end of 2015) for the same number of
>> +cores and, thanks to the message-passing technology, it can be executed on
>> +clusters.")
>
> Maybe transform:
> "This tool will let the users to avoid the analysis of not necessary
> reads, reducing the time of subsequent procedures with the dataset
> (e.g., assemblies, mappings, etc.)."
>
> into:
> "This tool lets users avoid the analysis of unnecesarry reads, reducing
> the time of subsequent procedures with the dataset (e.g., assemblies,
> mappings, etc.)."

Yes, I should change this to make this read like proper English :)
Thanks for taking a look!

~~ Ricardo