debian/0000775000000000000000000000000012253222633007170 5ustar debian/rules0000775000000000000000000000040612212757662010262 0ustar #!/usr/bin/make -f export DH_OPTIONS %: dh $@ override_dh_auto_configure: dh_auto_configure -- --with-mpi=/usr/lib/openmpi --disable-popcnt override_dh_auto_build: dh_auto_build --parallel override_dh_auto_install: dh_auto_install --destdir=debian/tmp debian/watch0000664000000000000000000000010312212757662010225 0ustar version=3 http://www.bcgsc.ca/downloads/abyss/ abyss-(.+)\.tar\.gz debian/changelog0000664000000000000000000000631612253222633011050 0ustar abyss (1.3.6-1build1) trusty; urgency=medium * No-change rebuild for libopenmpi1.3 -> libopenmpi1.6 transition. -- Logan Rosen Sat, 14 Dec 2013 22:43:43 -0500 abyss (1.3.6-1) unstable; urgency=low * Team upload (Closes: #722072). e05ee57 Imported Upstream version 1.3.5 b391f1f Imported Upstream version 1.3.6 (Closes: #702440) 7edc28b Signal the use of git-buildpackage with this configuration file. a3beaac Normalised source package control file with config-model-edit. dd86394 Conforms with Policy version 3.9.4. 71d42ad Normalised VCS URLs. -- Charles Plessy Sun, 08 Sep 2013 11:36:44 +0900 abyss (1.3.4-4) unstable; urgency=low * Team upload. * Fix FTBFS with gcc-4.8, -Werror=unused-local-typedefs. * Enable parallel build. -- Dmitrijs Ledkovs Mon, 01 Jul 2013 21:06:59 +0100 abyss (1.3.4-3) unstable; urgency=low * Disable POPCNT Closes: #697344 * Add debian/README.debian to inform users about this change asking for some comparison of the speed to consider other means for better performance -- Andreas Tille Fri, 04 Jan 2013 11:07:10 +0100 abyss (1.3.4-2) unstable; urgency=low * Team upload * debian/upstream: BibTeX compliant authors -- Andreas Tille Fri, 01 Jun 2012 08:38:29 +0200 abyss (1.3.4-1) unstable; urgency=low * New upstream release. * debian/copyright: Add CityHash, which has an Expat license. * debian/control: Bump Standards-Version to 3.9.3.1. -- Shaun Jackman Thu, 31 May 2012 11:39:13 -0700 abyss (1.3.3-2) unstable; urgency=low * debian/control: - Team maintenance in Debian Med team - Moved packaging to Git * debian/upstream: Add citation information * debhelper 9 (control+compat) * debian/copyright: Add github as another location for obtaining the source -- Andreas Tille Sun, 01 Apr 2012 08:44:48 +0200 abyss (1.3.3-1) unstable; urgency=low * New upstream release. * Some components are dual-licensed BCCA-Academic or GPL-3+. * Bump Standards-Version to 3.9.3. -- Shaun Jackman Tue, 13 Mar 2012 15:43:49 -0700 abyss (1.3.2-1) unstable; urgency=low * New upstream release. -- Shaun Jackman Tue, 13 Dec 2011 17:04:24 -0800 abyss (1.3.1-1) unstable; urgency=low * New upstream release. -- Shaun Jackman Mon, 24 Oct 2011 11:32:59 -0700 abyss (1.3.0-1) unstable; urgency=low * New upstream release. * Add libboost-graph-dev to Build-Depends. -- Shaun Jackman Sun, 11 Sep 2011 10:00:13 -0700 abyss (1.2.7-3) unstable; urgency=low * Align/Aligner.cpp, Scaffold/scaffold.cc: Fix FTBFS bug for GCC 4.6. -- Shaun Jackman Mon, 15 Aug 2011 11:07:19 -0700 abyss (1.2.7-2) unstable; urgency=low * debian/control: Add `XS-Autobuild: yes'. Suggest openmpi-bin. * debian/copyright: Change `Format-Specification' to `Format'. -- Shaun Jackman Thu, 21 Jul 2011 09:55:52 -0700 abyss (1.2.7-1) unstable; urgency=low * Initial release. Closes: #631534. -- Shaun Jackman Fri, 24 Jun 2011 12:16:36 -0700 debian/upstream0000664000000000000000000000071412212757662010767 0ustar Name: ABySS Reference: Author: Jared T. Simpson and Kim Wong and Shaun D. Jackman and Jacqueline E. Schein and Steven J.M. Jones and İnanç Birol Title: "ABySS: A parallel assembler for short read sequence data" Journal: Genome Research Year: 2009 Volume: 19 Number: 6 Pages: 1117-23 PMID: 19251739 DOI: 10.1101/gr.089532.108 URL: http://genome.cshlp.org/content/19/6/1117 eprint: http://genome.cshlp.org/content/19/6/1117.full.pdf+html debian/compat0000664000000000000000000000000212212757662010400 0ustar 9 debian/copyright0000664000000000000000000004414512212760722011134 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: ABySS Upstream-Contact: Shaun Jackman Source: http://www.bcgsc.ca/downloads/abyss/abyss-1.3.6.tar.gz License: BCCA-Academic Debian may redistribute this software package. . BC CANCER AGENCY SOFTWARE LICENSE AGREEMENT (ACADEMIC USE) CAREFULLY READ THE FOLLOWING TERMS AND CONDITIONS. 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BCCA, at its sole discretion may assign this Agreement without notice to You. Files: * Copyright: Copyright 2013 Genome Sciences Centre License: BCCA-Academic Files: Common/* DistanceEst/* ParseAligns/* Copyright: Copyright 2012 Genome Sciences Centre License: BCCA-Academic or GPL-3+ Files: Common/cholesky.hpp Copyright: Copyright 2005 Gunter Winkler, Konstantin Kutzkow License: LGPL-2.1+ Files: Common/city.cc Common/city.h Copyright: Copyright 2011 Google, Inc. License: Expat Files: dialign/* Copyright: Copyright 2008 Amarendran R. Subramanian License: LGPL-2.1+ License: LGPL-2.1+ On Debian systems, see `/usr/share/common-licenses/LGPL-2.1'. . This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. . This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA . Amarendran R. Subramanian, hereby disclaims all copyright interest in the DIALIGN-TX (a multiple sequence alignment algorithm) written by Amarendran R. Subramanian. . Amarendran R. Subramanian, 2004-2008 . DIALIGN-TX has been co-authored by Volker Menrad and Dorothea Emig. . Research work using DIALIGN-TX should cite: . DIALIGN-TX: improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern, Algorithms for Molecular Biology 3:6, 2008 . DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern, BMC Bioinformatics 6:66, 2005 Files: FMIndex/bit_array.h Copyright: Copyright 2010 Daisuke Okanohara License: BSD-3-clause Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . Redistributions of source code must retain the above Copyright notice, this list of conditions and the following disclaimer. . Redistributions in binary form must reproduce the above Copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . Neither the name of the authors nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. Files: FMIndex/sais.hxx Copyright: Copyright 2010 Yuta Mori License: Expat License: Expat Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. License: GPL-3+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the full text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'. debian/source/0000775000000000000000000000000012212757662010502 5ustar debian/source/format0000664000000000000000000000001412212757662011710 0ustar 3.0 (quilt) debian/manpages0000664000000000000000000000001012212757662010707 0ustar doc/*.1 debian/README.Debian0000664000000000000000000000123512212757662011244 0ustar Abyss for Debian ---------------- Due to http://bugs.debian.org/697344 this package was compiled using --disable-popcnt. If you need to profit from extra speed enhancement you could create a local package by doing the following: $ apt-get source abyss $ dch -i local build enabling POPCNT $ vi debian/rules remove '--disable-popcnt' from configure options $ debuild $ dpkg -i ../abyss*.deb Please inform us (= Debian Med team) about the gain of speed compared to the packaged version to enable us to try some better means to get the best out of your hardware. -- Andreas Tille Fri, 04 Jan 2013 11:07:10 +0100 debian/install0000664000000000000000000000006112212757662010570 0ustar usr/bin/abyss-pe usr/bin usr/bin/* usr/lib/abyss debian/control0000664000000000000000000000235112212761121010567 0ustar Source: abyss Maintainer: Debian Med Packaging Team Uploaders: Shaun Jackman , Andreas Tille Section: non-free/science XS-Autobuild: yes Priority: optional Build-Depends: debhelper (>= 9), autotools-dev, libboost-graph-dev, libopenmpi-dev, libsparsehash-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/abyss.git Vcs-Git: git://anonscm.debian.org/debian-med/abyss.git Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss Package: abyss Architecture: any Depends: make, ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends} Suggests: openmpi-bin Description: de novo, parallel, sequence assembler for short reads ABySS is a de novo, parallel, sequence assembler that is designed for short reads. It may be used to assemble genome or transcriptome sequence data. Parallelization is achieved using MPI, OpenMP and pthread. . To cite your use of ABySS, please reference ABySS: A parallel assembler for short read sequence data. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. Genome Research, 2009-June. debian/docs0000664000000000000000000000006312212757662010054 0ustar README.md README.css README.html doc/flowchart.pdf debian/gbp.conf0000664000000000000000000000031412212757662010617 0ustar # This source package is managed with git-buildpackage and pristine-tar. [DEFAULT] # use pristine-tar: pristine-tar = True [dch] # include 7 digits of the commit id in the changelog enty: id-length = 7 debian/patches/0000775000000000000000000000000012212757662010631 5ustar debian/patches/series0000664000000000000000000000002612212757662012044 0ustar abyss-pe gcc4.8.patch debian/patches/gcc4.8.patch0000664000000000000000000000762412212757662012651 0ustar Description: -Werror=unused-local-typedefs Author: Dmitrijs Ledkovs --- a/Graph/ContigGraphAlgorithms.h +++ b/Graph/ContigGraphAlgorithms.h @@ -199,7 +199,6 @@ template OutIt assemble_if(Graph& g, OutIt out, Predicate pred0) { - typedef typename Graph::vertex_descriptor vertex_descriptor; typedef typename Graph::vertex_iterator vertex_iterator; // pred(e) = !isPalindrome(e) && pred0(e) binary_compose, --- a/Graph/SAMIO.h +++ b/Graph/SAMIO.h @@ -23,8 +23,6 @@ vertex_property_type; typedef typename graph_traits::edge_iterator edge_iterator; - typedef typename edge_property::type - edge_property_type; out << "@HD\tVN:1.0\n" "@PG\tID:" << program << "\tVN:" VERSION "\t" --- a/Graph/DotIO.h +++ b/Graph/DotIO.h @@ -33,8 +33,6 @@ typename graph_traits::vertex_descriptor u, const EdgeProp*) { - typedef typename graph_traits::vertex_descriptor - vertex_descriptor; typedef typename graph_traits::out_edge_iterator out_edge_iterator; typedef typename edge_property::type edge_property_type; --- a/Map/overlap.cc +++ b/Map/overlap.cc @@ -272,7 +272,6 @@ /** Read contigs and add vertices to the graph. */ static void addVertices(const string& path, Graph& g) { - typedef vertex_property::type VP; if (opt::verbose > 0) cerr << "Reading `" << path << "'...\n"; ifstream in(path.c_str()); --- a/MergePaths/PathConsensus.cpp +++ b/MergePaths/PathConsensus.cpp @@ -184,8 +184,6 @@ static ContigPaths readPaths(const string& inPath, vector& ids, vector& isAmb) { - typedef graph_traits::vertex_descriptor V; - assert(ids.empty()); assert(isAmb.empty()); assert(g_ambpath_contig.empty()); --- a/Graph/PopBubbles.h +++ b/Graph/PopBubbles.h @@ -161,7 +161,6 @@ void scaffoldBubble(Graph& g, const Bubble& bubble) { typedef graph_traits GTraits; - typedef typename GTraits::adjacency_iterator Ait; typedef typename GTraits::vertex_descriptor V; assert(bubble.size() > 2); --- a/PopBubbles/PopBubbles.cpp +++ b/PopBubbles/PopBubbles.cpp @@ -464,7 +464,6 @@ */ static void scaffoldBubble(Graph& g, const Bubble& bubble) { - typedef graph_traits::adjacency_iterator Ait; typedef graph_traits::vertex_descriptor V; assert(opt::scaffold); assert(bubble.size() > 2); --- a/Common/cholesky.hpp +++ b/Common/cholesky.hpp @@ -53,8 +53,6 @@ { using namespace ublas; - typedef typename MATRIX::value_type T; - assert( A.size1() == A.size2() ); assert( A.size1() == L.size1() ); assert( A.size2() == L.size2() ); @@ -95,8 +93,6 @@ { using namespace ublas; - typedef typename MATRIX::value_type T; - const MATRIX& A_c(A); const size_t n = A.size1(); --- a/Scaffold/drawgraph.cc +++ b/Scaffold/drawgraph.cc @@ -164,7 +164,6 @@ typedef graph_traits::edge_iterator Eit; typedef graph_traits::vertex_descriptor V; typedef graph_traits::vertex_iterator Vit; - typedef edge_bundle_type::type EP; Graph g; if (optind < argc) { --- a/Scaffold/scaffold.cc +++ b/Scaffold/scaffold.cc @@ -121,8 +121,6 @@ static void filterGraph(Graph& g, unsigned minContigLength) { typedef graph_traits GTraits; - typedef GTraits::edge_descriptor E; - typedef GTraits::edge_iterator Eit; typedef GTraits::vertex_descriptor V; typedef GTraits::vertex_iterator Vit; @@ -237,8 +235,6 @@ */ static void pruneTips(Graph& g) { - typedef graph_traits::vertex_descriptor V; - /** Identify the tips. */ size_t n = 0; pruneTips(g, CountingOutputIterator(n)); --- a/FilterGraph/FilterGraph.cpp +++ b/FilterGraph/FilterGraph.cpp @@ -279,8 +279,6 @@ { typedef graph_traits GTraits; typedef GTraits::vertex_descriptor V; - typedef GTraits::out_edge_iterator OEit; - typedef GTraits::in_edge_iterator IEit; vector out; out.reserve(sc.size()); debian/patches/abyss-pe0000664000000000000000000000055212212757662012301 0ustar --- abyss-1.3.3.orig/bin/abyss-pe 2012-03-13 16:24:07.000000000 -0700 +++ abyss-1.3.3/bin/abyss-pe 2012-03-13 16:24:46.000000000 -0700 @@ -2,6 +2,8 @@ # Run the ABySS assembler. # Written by Shaun Jackman . +PATH:=/usr/lib/abyss:${PATH} + # Set pipefail to require that all commands of a pipe must succeed. SHELL=/bin/bash -o pipefail