From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add GDSL and bwa-pssm. Date: Mon, 29 Feb 2016 15:14:43 +0100 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:35002) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aaOb9-0006x5-Io for guix-devel@gnu.org; Mon, 29 Feb 2016 09:14:56 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aaOb6-0007zc-Az for guix-devel@gnu.org; Mon, 29 Feb 2016 09:14:55 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:49507) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aaOb5-0007zI-UJ for guix-devel@gnu.org; Mon, 29 Feb 2016 09:14:52 -0500 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 2E4FB38051C for ; Mon, 29 Feb 2016 15:14:50 +0100 (CET) Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id bnQzfg4OuMSN for ; Mon, 29 Feb 2016 15:14:44 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Mon, 29 Feb 2016 15:14:44 +0100 (CET) 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-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel --=-=-= Content-Type: text/x-patch; charset="utf-8" Content-Disposition: inline; filename="0001-gnu-Add-gdsl.patch" Content-Transfer-Encoding: quoted-printable >From 6e4a02b441ecfc5cbedfdcd7f8823204ac1a747c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 29 Feb 2016 15:13:12 +0100 Subject: [PATCH 1/2] gnu: Add gdsl. * gnu/packages/datastructures.scm (gdsl): New variable. --- gnu/packages/datastructures.scm | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/gnu/packages/datastructures.scm b/gnu/packages/datastructure= s.scm index 3614900..74b9fff 100644 --- a/gnu/packages/datastructures.scm +++ b/gnu/packages/datastructures.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright =C2=A9 2015 Ricardo Wurmus +;;; Copyright =C2=A9 2015, 2016 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -23,6 +23,29 @@ #:use-module (guix download) #:use-module (guix build-system gnu)) =20 +(define-public gdsl + (package + (name "gdsl") + (version "1.8") + (source (origin + (method url-fetch) + (uri (string-append "http://download.gna.org/gdsl/" + "gdsl-" version ".tar.gz")) + (sha256 + (base32 + "1v64jvlnj8jfpphphgjgb36p0kv50kwfyqncf0y12f16v8ydyiaw"))= )) + (build-system gnu-build-system) + (home-page "http://home.gna.org/gdsl/") + (synopsis "Generic data structures library") + (description "The Generic Data Structures Library (GDSL) is a collec= tion +of routines for generic data structures manipulation. It is a re-entran= t +library fully written from scratch in pure ANSI C. It is designed to of= fer +for C programmers common data structures with powerful algorithms, and h= idden +implementation. Available structures are lists, queues, stacks, hash ta= bles, +binary trees, binary search trees, red-black trees, 2D arrays, permutati= ons +and heaps.") + (license license:gpl2+))) + (define-public sparsehash (package (name "sparsehash") --=20 2.1.0 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0002-gnu-Add-bwa-pssm.patch" >From 7208e8b25ff14deac88a133a9c2eb6d5a4ab6a98 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 29 Feb 2016 15:13:52 +0100 Subject: [PATCH 2/2] gnu: Add bwa-pssm. * gnu/packages/bioinformatics.scm (bwa-pssm): New variable. --- gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6df7d5c..c81126e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -41,6 +41,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages cpio) #:use-module (gnu packages curl) + #:use-module (gnu packages datastructures) #:use-module (gnu packages file) #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) @@ -773,6 +774,35 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.") (license license:gpl3+))) +(define-public bwa-pssm + (package (inherit bwa) + (name "bwa-pssm") + (version "0.5.11") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/" + "archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg")))) + (build-system gnu-build-system) + (inputs + `(("gdsl" ,gdsl) + ("zlib" ,zlib) + ("perl" ,perl))) + (home-page "http://bwa-pssm.binf.ku.dk/") + (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper") + (description + "BWA-PSSM is a probabilistic short genomic sequence read aligner based on +the use of @dfn{position specific scoring matrices} (PSSM). Like many of the +existing aligners it is fast and sensitive. Unlike most other aligners, +however, it is also adaptible in the sense that one can direct the alignment +based on known biases within the data set. It is coded as a modification of +the original BWA alignment program and shares the genome index structure as +well as many of the command line options.") + (license license:gpl3+))) + (define-public python2-bx-python (package (name "python2-bx-python") -- 2.1.0 --=-=-=--