From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH 16/22] gnu: Add bpp-phyl. Date: Wed, 27 Jul 2016 22:54:17 +1000 Message-ID: <487eaba50a6e5a5c3b8d1c30eaa983fd97dc724a.1469622379.git.donttrustben@gmail.com> References: <20160727125423.7768-1-donttrustben@gmail.com> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:54990) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bSON3-0000Ii-O1 for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:35 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bSON0-0004eR-5G for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:32 -0400 Received: from mail-pa0-x242.google.com ([2607:f8b0:400e:c03::242]:33040) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bSOMz-0004eK-U5 for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:30 -0400 Received: by mail-pa0-x242.google.com with SMTP id q2so1755459pap.0 for ; Wed, 27 Jul 2016 05:55:29 -0700 (PDT) Received: from localhost.localdomain ([103.25.181.216]) by smtp.googlemail.com with ESMTPSA id o80sm9177941pfa.67.2016.07.27.05.55.25 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-SHA bits=128/128); Wed, 27 Jul 2016 05:55:27 -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-phyl): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4ca890c..803dae9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -503,6 +503,43 @@ 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-phyl + ;; 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 "0c07167b629f68b569bf274d1ad0c4af83276ae2")) + (package + (name "bpp-phyl") + (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-phyl") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh")))) + (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) + ("bpp-seq" ,bpp-seq) + ;; GCC 4.8 fails due to an 'internal compiler error', so we use a more + ;; modern GCC. + ("gcc" ,gcc-5))) + (home-page "http://biopp.univ-montp2.fr") + (synopsis "Bio++ phylogenetic Library") + (description + "Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. This +library provides phylogenetics-related modules.") + (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. -- 2.9.1