From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH 18/22] gnu: Add bppsuite. Date: Wed, 27 Jul 2016 22:54:19 +1000 Message-ID: References: <20160727125423.7768-1-donttrustben@gmail.com> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:55209) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bSONA-0000Of-LB for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:42 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bSON6-0004ha-70 for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:40 -0400 Received: from mail-pa0-x243.google.com ([2607:f8b0:400e:c03::243]:33043) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bSON5-0004h5-RN for guix-devel@gnu.org; Wed, 27 Jul 2016 08:55:36 -0400 Received: by mail-pa0-x243.google.com with SMTP id q2so1755563pap.0 for ; Wed, 27 Jul 2016 05:55:35 -0700 (PDT) Received: from localhost.localdomain ([103.25.181.216]) by smtp.googlemail.com with ESMTPSA id o80sm9177941pfa.67.2016.07.27.05.55.31 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-SHA bits=128/128); Wed, 27 Jul 2016 05:55:33 -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 (bppsuite): New variable. --- gnu/packages/bioinformatics.scm | 42 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5dfc637..5ea2240 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -51,11 +51,13 @@ #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) #:use-module (gnu packages gd) + #:use-module (gnu packages groff) #:use-module (gnu packages image) #:use-module (gnu packages java) #:use-module (gnu packages linux) #:use-module (gnu packages logging) #:use-module (gnu packages machine-learning) + #:use-module (gnu packages man) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages ncurses) @@ -70,6 +72,7 @@ #:use-module (gnu packages ruby) #:use-module (gnu packages statistics) #:use-module (gnu packages tbb) + #:use-module (gnu packages texinfo) #:use-module (gnu packages textutils) #:use-module (gnu packages time) #:use-module (gnu packages tls) @@ -607,6 +610,45 @@ analysis, phylogenetics, molecular evolution and population genetics. This library provides sequence-related modules.") (license license:cecill-c)))) +(define-public bppsuite + ;; 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 "c516147f57aa50961121cd505bed52cd7603698b")) + (package + (name "bppsuite") + (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/bppsuite") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb")))) + (build-system cmake-build-system) + (arguments + `(#:parallel-build? #f + #:tests? #f)) ; There are no tests. + (native-inputs + `(("groff" ,groff) + ("man-db" ,man-db) + ("texinfo" ,texinfo))) + (inputs + `(("bpp-core" ,bpp-core) + ("bpp-seq" ,bpp-seq) + ("bpp-phyl" ,bpp-phyl) + ("bpp-phyl" ,bpp-popgen) + ("gcc" ,gcc-5))) + (home-page "http://biopp.univ-montp2.fr") + (synopsis "Bioinformatics tools written with the Bio++ libraries") + (description + "Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. This +package provides command line tools using the Bio++ library.") + (license license:cecill-c)))) + (define-public blast+ (package (name "blast+") -- 2.9.1