From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH 21/22] gnu: Add raxml. Date: Wed, 27 Jul 2016 22:54:22 +1000 Message-ID: References: <20160727125423.7768-1-donttrustben@gmail.com> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:55349) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bSONH-0000Ta-9E for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:50 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bSONE-0004lI-RS for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:46 -0400 Received: from mail-pa0-x244.google.com ([2607:f8b0:400e:c03::244]:33048) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bSONE-0004kx-Ej for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:44 -0400 Received: by mail-pa0-x244.google.com with SMTP id q2so1755731pap.0 for ; Wed, 27 Jul 2016 05:55:44 -0700 (PDT) Received: from localhost.localdomain ([103.25.181.216]) by smtp.googlemail.com with ESMTPSA id o80sm9177941pfa.67.2016.07.27.05.55.40 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-SHA bits=128/128); Wed, 27 Jul 2016 05:55:42 -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 (raxml): New variable. --- gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ea37a93..4e599a7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3297,6 +3297,46 @@ format. It runs quickly, in an unsupervised fashion, handles gaps, handles partial genes, and identifies translation initiation sites.") (license license:gpl3+))) +(define-public raxml + (package + (name "raxml") + (version "8.2.9") + (source + (origin + (method url-fetch) + (uri + (string-append + "https://github.com/stamatak/standard-RAxML/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1pv8p2fy67y21a9y4cm7xpvxqjwz2v4201flfjshdq1p8j52rqf7")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests. + ;; Use 'standard' Makefile rather than SSE or AVX ones. + #:make-flags (list "-f" "Makefile.HYBRID.gcc") + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (executable "raxmlHPC-HYBRID")) + (install-file executable bin) + (symlink (string-append bin "/" executable) "raxml")) + #t))))) + (inputs + `(("openmpi" ,openmpi))) + (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html") + (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees") + (description + "RAxML is a tool for phylogenetic analysis and post-analysis of large +phylogenies.") + (license license:gpl2+))) + (define-public rsem (package (name "rsem") -- 2.9.1