Re: [PATCH] gnu: Add ParDRe.

[Ricardo Wurmus]

Ricardo Wurmus <address@hidden> writes:

> Roel Janssen <address@hidden> 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!

Pushed with the fixed synopsis and with a couple of changes to the
description.

~~ Ricardo