From mboxrd@z Thu Jan 1 00:00:00 1970 From: Roel Janssen Subject: Re: [PATCH] gnu: Add ParDRe. Date: Mon, 23 May 2016 11:29:10 +0200 Message-ID: <87d1odw2ah.fsf@gnu.org> References: <1463994575-2329-1-git-send-email-ricardo.wurmus@mdc-berlin.de> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:40618) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1b4mAh-0004yX-AS for guix-devel@gnu.org; Mon, 23 May 2016 05:29:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1b4mAd-0008BC-4e for guix-devel@gnu.org; Mon, 23 May 2016 05:29:10 -0400 In-reply-to: <1463994575-2329-1-git-send-email-ricardo.wurmus@mdc-berlin.de> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Ricardo Wurmus Cc: guix-devel@gnu.org 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