From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH 15/22] gnu: Add bpp-seq. Date: Wed, 27 Jul 2016 22:54:16 +1000 Message-ID: References: <20160727125423.7768-1-donttrustben@gmail.com> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:54873) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bSOMz-0000ES-8z for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:32 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bSOMx-0004cN-2R for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:28 -0400 Received: from mail-pf0-x241.google.com ([2607:f8b0:400e:c00::241]:33476) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bSOMw-0004bl-RS for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:26 -0400 Received: by mail-pf0-x241.google.com with SMTP id i6so1842558pfe.0 for ; Wed, 27 Jul 2016 05:55:26 -0700 (PDT) Received: from localhost.localdomain ([103.25.181.216]) by smtp.googlemail.com with ESMTPSA id o80sm9177941pfa.67.2016.07.27.05.55.23 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-SHA bits=128/128); Wed, 27 Jul 2016 05:55:24 -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 (bpp-seq): New variable. --- gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4fb23a4..4ca890c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -503,6 +503,40 @@ Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.") (license license:cecill-c)))) +(define-public bpp-seq + ;; The last release was in 2014 and the recommended way to install from source + ;; is to clone the git repository, so we do this. + ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page + (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33")) + (package + (name "bpp-seq") + (version (string-append "2.2.0-1." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "http://biopp.univ-montp2.fr/git/bpp-seq") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2")))) + (build-system cmake-build-system) + (arguments + `(#:parallel-build? #f + ;; If out-of-source, test data is not copied into the build directory + ;; so the tests fail. + #:out-of-source? #f)) + (inputs + `(("bpp-core" ,bpp-core) + ("gcc" ,gcc-5))) ; Use GCC 5 as per 'bpp-core'. + (home-page "http://biopp.univ-montp2.fr") + (synopsis "Bio++ sequence library") + (description + "Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. This +library provides sequence-related modules.") + (license license:cecill-c)))) + (define-public blast+ (package (name "blast+") -- 2.9.1