From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:58954) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ec8zG-0003QC-Ah for guix-patches@gnu.org; Thu, 18 Jan 2018 07:08:07 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ec8zD-0003Z3-Jx for guix-patches@gnu.org; Thu, 18 Jan 2018 07:08:06 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:53131) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1ec8zD-0003Yx-C4 for guix-patches@gnu.org; Thu, 18 Jan 2018 07:08:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ec8zD-00063u-7J for guix-patches@gnu.org; Thu, 18 Jan 2018 07:08:03 -0500 Subject: [bug#30152] [PATCH 2/4] gnu: Add libdivsufsort. Resent-Message-ID: From: Ricardo Wurmus Date: Thu, 18 Jan 2018 10:28:28 +0100 Message-Id: <20180118092830.22110-2-rekado@elephly.net> In-Reply-To: <20180118092830.22110-1-rekado@elephly.net> References: <20180118092830.22110-1-rekado@elephly.net> List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 30152@debbugs.gnu.org Cc: Ricardo Wurmus * gnu/packages/bioinformatics.scm (libdivsufsort): New variable. --- gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f5e32ffa4..c820f87c0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11132,3 +11132,31 @@ code that is used in the Cufflinks codebase. The goal of this library is to provide this functionality without the necessity of drawing in a heavy-weight dependency like SeqAn.") (license (license:x11-style "http://www.boost.org/LICENSE_1_0.txt")))) + +(define-public libdivsufsort + (package + (name "libdivsufsort") + (version "2.0.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/y-256/libdivsufsort.git") + (commit version))) + (sha256 + (base32 + "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2")))) + (build-system cmake-build-system) + (arguments + '(#:tests? #f ; there are no tests + #:configure-flags + ;; Needed for rapmap and sailfish. + '("-DBUILD_DIVSUFSORT64=ON"))) + (home-page "https://github.com/y-256/libdivsufsort") + (synopsis "Lightweight suffix-sorting library") + (description "libdivsufsort is a software library that implements a +lightweight suffix array construction algorithm. This library provides a +simple and an efficient C API to construct a suffix array and a +Burrows-Wheeler transformed string from a given string over a constant-size +alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1) +bytes of memory space, where n is the length of the string.") + (license license:expat))) -- 2.15.0