From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH 20/22] gnu: Add prank. Date: Wed, 27 Jul 2016 22:54:21 +1000 Message-ID: <00cdf65fb69d021379461d6589059f5f45884435.1469622379.git.donttrustben@gmail.com> References: <20160727125423.7768-1-donttrustben@gmail.com> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:55286) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bSONE-0000R7-JG for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:46 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bSONB-0004k2-UB for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:43 -0400 Received: from mail-pa0-x244.google.com ([2607:f8b0:400e:c03::244]:34486) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bSONB-0004je-Ea for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:41 -0400 Received: by mail-pa0-x244.google.com with SMTP id hh10so1762703pac.1 for ; Wed, 27 Jul 2016 05:55:41 -0700 (PDT) Received: from localhost.localdomain ([103.25.181.216]) by smtp.googlemail.com with ESMTPSA id o80sm9177941pfa.67.2016.07.27.05.55.37 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-SHA bits=128/128); Wed, 27 Jul 2016 05:55:39 -0700 (PDT) In-Reply-To: <20160727125423.7768-1-donttrustben@gmail.com> In-Reply-To: References: 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: guix-devel@gnu.org * gnu/packages/bioinformatics.scm (prank): New variable. --- gnu/packages/bioinformatics.scm | 52 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 14ac57f..ea37a93 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3176,6 +3176,58 @@ the phenotype as it models the data.") generated using the PacBio Iso-Seq protocol.") (license license:bsd-3)))) +(define-public prank + (package + (name "prank") + (version "150803") + (source (origin + (method url-fetch) + (uri (string-append + "http://wasabiapp.org/download/prank/prank.source." + version ".tgz")) + (sha256 + (base32 + "0am4z94fs3w2n5xpfls9zda61vq7qqz4q2i7b9hlsxz5q4j3kfm4")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'enter-src-dir + (lambda _ + (chdir "src") + #t)) + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (man (string-append out "/share/man/man1")) + (path (string-append + (assoc-ref %build-inputs "mafft") "/bin:" + (assoc-ref %build-inputs "exonerate") "/bin:" + (assoc-ref %build-inputs "bppsuite") "/bin"))) + (install-file "prank" bin) + (wrap-program (string-append bin "/prank") + `("PATH" ":" prefix (,path))) + (install-file "prank.1" man)) + #t))))) + (inputs + `(("mafft" ,mafft) + ("exonerate" ,exonerate) + ("bppsuite" ,bppsuite))) + (home-page "http://wasabiapp.org/software/prank/") + (synopsis "Probabilistic multiple sequence alignment program") + (description + "PRANK is a probabilistic multiple sequence alignment program for DNA, +codon and amino-acid sequences. It is based on a novel algorithm that treats +insertions correctly and avoids over-estimation of the number of deletion +events. In addition, PRANK borrows ideas from maximum likelihood methods used +in phylogenetics and correctly takes into account the evolutionary distances +between sequences. Lastly, PRANK allows for defining a potential structure +for sequences to be aligned and then, simultaneously with the alignment, +predicts the locations of structural units in the sequences.") + (license license:gpl2+))) + (define-public pyicoteo (package (name "pyicoteo") -- 2.9.1