Re: [PATCH] gnu: Add ParDRe.

[Roel Janssen]

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.

> +    (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.)."

> +    (home-page "https://sourceforge.net/projects/pardre/";)
> +    (license license:gpl3+)))
> +
>  (define-public bio-locus
>    (package
>      (name "bio-locus")

Kind regards,
Roel Janssen