From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH 14/22] gnu: Add bpp-core. Date: Wed, 27 Jul 2016 22:54:15 +1000 Message-ID: <2beb318e025e88bf0bb9d81f1a12c49c75c335b3.1469622379.git.donttrustben@gmail.com> References: <20160727125423.7768-1-donttrustben@gmail.com> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:54785) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bSOMv-0000Bl-GE for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:26 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bSOMu-0004Zp-5l for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:25 -0400 Received: from mail-pf0-x243.google.com ([2607:f8b0:400e:c00::243]:33473) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bSOMt-0004ZF-Vb for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:24 -0400 Received: by mail-pf0-x243.google.com with SMTP id i6so1842498pfe.0 for ; Wed, 27 Jul 2016 05:55:23 -0700 (PDT) Received: from localhost.localdomain ([103.25.181.216]) by smtp.googlemail.com with ESMTPSA id o80sm9177941pfa.67.2016.07.27.05.55.20 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-SHA bits=128/128); Wed, 27 Jul 2016 05:55:21 -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-core): New variable. --- gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6065a00..4fb23a4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -470,6 +470,39 @@ into separate processes; and more.") (inputs `(("python2-numpy" ,python2-numpy))))) +(define-public bpp-core + ;; 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 "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582")) + (package + (name "bpp-core") + (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-core") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j")))) + (build-system cmake-build-system) + (arguments + `(#:parallel-build? #f)) + (inputs + `(("gcc" ,gcc-5))) ; Compilation of bpp-phyl fails with GCC 4.9 so we + ; compile all of the bpp packages with GCC 5. + (home-page "http://biopp.univ-montp2.fr") + (synopsis "C++ libraries for Bioinformatics") + (description + "Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. It is +Object Oriented and is designed to be both easy to use and computer efficient. +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 blast+ (package (name "blast+") -- 2.9.1