From mboxrd@z Thu Jan 1 00:00:00 1970 From: Marius Bakke Subject: [PATCH] gnu: Add mash. Date: Tue, 30 Aug 2016 18:54:49 +0100 Message-ID: <87h9a2yweu.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me> Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:57588) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1benFY-0004vc-Ri for guix-devel@gnu.org; Tue, 30 Aug 2016 13:55:06 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1benFT-0008Hm-TM for guix-devel@gnu.org; Tue, 30 Aug 2016 13:55:03 -0400 Received: from out4-smtp.messagingengine.com ([66.111.4.28]:38135) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1benFR-0008Fz-Go for guix-devel@gnu.org; Tue, 30 Aug 2016 13:54:59 -0400 Received: from compute4.internal (compute4.nyi.internal [10.202.2.44]) by mailout.nyi.internal (Postfix) with ESMTP id C495C20691 for ; Tue, 30 Aug 2016 13:54:50 -0400 (EDT) Received: from localhost (05430ba6.skybroadband.com [5.67.11.166]) by mail.messagingengine.com (Postfix) with ESMTPA id 5968FF29D3 for ; Tue, 30 Aug 2016 13:54:50 -0400 (EDT) Content-Disposition: inline; filename=0001-gnu-Add-mash.patch 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 >From 20974083333c8e94d10423d4a156caa5298d6dcb Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 30 Aug 2016 18:49:21 +0100 Subject: [PATCH 1/1] gnu: Add mash. * gnu/packages/bioinformatics.scm (mash): New variable. --- gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ed20b56..9b96d37 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -76,6 +76,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages readline) #:use-module (gnu packages ruby) + #:use-module (gnu packages serialization) #:use-module (gnu packages statistics) #:use-module (gnu packages tbb) #:use-module (gnu packages tex) @@ -3046,6 +3047,58 @@ sequences).") "http://mafft.cbrc.jp/alignment/software/license.txt" "BSD-3 with different formatting")))) +(define-public mash + (package + (name "mash") + (version "1.1.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/marbl/mash/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "08znbvqq5xknfhmpp3wcj574zvi4p7i8zifi67c9qw9a6ikp42fj")) + (modules '((guix build utils))) + (snippet + ;; Delete bundled kseq. + ;; TODO: Also delete bundled murmurhash and open bloom filter. + '(delete-file "src/mash/kseq.h")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; No tests. + #:configure-flags + (list + (string-append "--with-capnp=" (assoc-ref %build-inputs "capnproto")) + (string-append "--with-gsl=" (assoc-ref %build-inputs "gsl"))) + #:make-flags (list "CC=gcc") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-includes + (lambda _ + (substitute* '("src/mash/Sketch.cpp" "src/mash/CommandFind.cpp") + (("^#include \"kseq\\.h\"") + "#include \"htslib/kseq.h\"")) + #t)) + (add-before 'configure 'autoconf + (lambda _ (zero? (system* "autoconf"))))))) + (native-inputs + `(("autoconf" ,autoconf) + ("capnproto" ,capnproto) + ("htslib" ,htslib))) + (inputs + `(("gsl" ,gsl) + ("zlib" ,zlib))) + (home-page "https://mash.readthedocs.io") + (synopsis "Fast genome and metagenome distance estimation using MinHash") + (description "Mash is a fast sequence distance estimator that uses the +MinHash algorithm and is designed to work with genomes and metagenomes in the +form of assemblies or reads.") + ;; Mash is distributed under 3-clause BSD, but includes software covered + ;; by other licenses. + (license (list license:bsd-3 license:public-domain license:cpl1.0)))) + (define-public metabat (package (name "metabat") -- 2.9.3