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Re: [PATCH] gnu: Add ParDRe.
From: |
Roel Janssen |
Subject: |
Re: [PATCH] gnu: Add ParDRe. |
Date: |
Mon, 23 May 2016 11:29:10 +0200 |
User-agent: |
mu4e 0.9.17; emacs 25.1.50.1 |
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