From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] gnu: Add ParDRe. Date: Mon, 23 May 2016 12:57:04 +0200 Message-ID: References: <1463994575-2329-1-git-send-email-ricardo.wurmus@mdc-berlin.de> <87d1odw2ah.fsf@gnu.org> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:57066) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1b4nXy-0002aT-6p for guix-devel@gnu.org; Mon, 23 May 2016 06:57:21 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1b4nXs-0001Dn-3o for guix-devel@gnu.org; Mon, 23 May 2016 06:57:16 -0400 In-Reply-To: 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: Roel Janssen Cc: guix-devel@gnu.org Ricardo Wurmus writes: > Roel Janssen 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