debian/0000775000000000000000000000000012253226566007201 5ustar debian/rules0000775000000000000000000000034412100005521010233 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) $(CPPFLAGS) -I/usr/lib/openmpi/include %: dh $@ --with autoreconf debian/watch0000664000000000000000000000015412076255230010223 0ustar version=3 https://launchpad.net/zalign https://launchpad.net/zalign/.*/\+download/zalign-([0-9.]+)\.tar\.gz debian/changelog0000664000000000000000000000051712253226562011052 0ustar zalign (0.9.1-1build1) trusty; urgency=medium * No-change rebuild for libopenmpi1.3 -> libopenmpi1.6 transition. -- Logan Rosen Sat, 14 Dec 2013 23:13:47 -0500 zalign (0.9.1-1) unstable; urgency=low * Initial release (Closes: #686000) -- Andreas Tille Thu, 21 Feb 2013 16:21:25 +0100 debian/upstream0000664000000000000000000000066712077543106010771 0ustar Reference: Author: Rodolfo Bezerra Batista and Azzedine Boukerche and Alba Cristina Magalhaes Alves de Melo Title: A parallel strategy for biological sequence alignment in restricted memory space Journal: Journal of Parallel and Distributed Computing Year: 2008 Volume: 68 Number: 4 Pages: 548--561 DOI: 10.1016/j.jpdc.2007.08.007 URL: http://www.sciencedirect.com/science/article/pii/S0743731507001530 issn: 0743-7315 debian/compat0000664000000000000000000000000212077536145010400 0ustar 9 debian/zalign.10000664000000000000000000000342112077541513010543 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10. .TH ZALIGN "1" "16. Aug 2009" "0.9.1" "User Commands" .SH NAME zalign \- parallel local alignment of biological sequences .SH SYNOPSIS .B zalign [\-s scores] [\-S split] [\-H hblk] [\-V vblk] file1 file2 .SH DESCRIPTION zAlign is a local sequence aligner, especially intended for use with large biological DNA sequences, with more than 1Mbp (Millions of base pairs). It uses the Smith-Waterman exact algorithm with affine gap cost function to perform this task. .SS "General options:" .TP \fB\-h\fR display this help and exit .TP \fB\-s\fR specify a comma\-separated list of scores to be used while calculating aligment matrices throughout the program. The list must be in the format "\-sMATCH,MISMATCH,GAP_OPEN,GAP_EXTENSION" (without quotes), and is parsed in this PRECISE order; no spaces are allowed between values. If there are any unspecified parameters, these are set to default values and a warning message is issued; exceeding parameters are discarded .SS "Stage 2 options:" .TP \fB\-S\fR (mpialign only) number of parts in which to split the alignment matrix; after this step a cyclic block model is applied, subdividing each part equally between all available nodes .TP \fB\-H\fR (mpialign only) number of horizontal subdivisions made by each node to its alignment submatrix; since this value defines block width, a good choice should allow two full matrix lines to fit the processor's cache pages, improving algorithm performance .TP \fB\-V\fR (mpialign only) number of vertical subdivisions made by each node to its alignment submatrix; this value directly affects the amount of internode communication and is used ONLY if 'split' is set to 1, otherwise it is set to the number of available nodes debian/copyright0000664000000000000000000000227112111434647011130 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: zalign Source: https://launchpad.net/zalign Files: * Copyright: 2006-2009 Rodolfo Bezerra Batista 2006-2009 Felipe Brant Scarel License: GPL-3.0+ Files: debian/* Copyright: 2012 Steffen Moeller 2013 Andreas Tille License: GPL-3.0+ License: GPL-3.0+ 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 package 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 program. If not, see . . On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". debian/source/0000775000000000000000000000000012076175650010501 5ustar debian/source/format0000664000000000000000000000001412016702075011676 0ustar 3.0 (quilt) debian/manpages0000664000000000000000000000001312077540125010703 0ustar debian/*.1 debian/control0000664000000000000000000000235712100003370010564 0ustar Source: zalign Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Build-Depends: debhelper (>= 9), autotools-dev, libopenmpi-dev, dh-autoreconf Standards-Version: 3.9.4 Homepage: https://launchpad.net/zalign Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/zalign/trunk/ Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/zalign/trunk Package: zalign Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: parallel local alignment of biological sequences zAlign is a local sequence aligner, especially intended for use with large biological DNA sequences, with more than 1Mbp (Millions of base pairs). It uses the Smith-Waterman exact algorithm with affine gap cost function to perform this task. . zAlign can be used both in distributed (clusters, for example) or standalone environments. Currently it has been tested on Linux and Sun Solaris, using both the MPICH (http://www.mcs.anl.gov/research/projects/mpi/mpich1/) and OpenMPI (http://www.open-mpi.org/) implementations. Ports for other Unix-like environments are highly considered. debian/mpialign.10000664000000000000000000000343112077541474011066 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10. .TH MPIALIGN "1" "16. Aug 2009" "0.9.1" "User Commands" .SH NAME mpialign \- parallel local alignment of biological sequences .SH SYNOPSIS .B mpialign [\-s scores] [\-S split] [\-H hblk] [\-V vblk] file1 file2 .SH DESCRIPTION mpiAlign is a local sequence aligner, especially intended for use with large biological DNA sequences, with more than 1Mbp (Millions of base pairs). It uses the Smith-Waterman exact algorithm with affine gap cost function to perform this task. .SS "General options:" .TP \fB\-h\fR display this help and exit .TP \fB\-s\fR specify a comma\-separated list of scores to be used while calculating aligment matrices throughout the program. The list must be in the format "\-sMATCH,MISMATCH,GAP_OPEN,GAP_EXTENSION" (without quotes), and is parsed in this PRECISE order; no spaces are allowed between values. If there are any unspecified parameters, these are set to default values and a warning message is issued; exceeding parameters are discarded .SS "Stage 2 options:" .TP \fB\-S\fR (mpialign only) number of parts in which to split the alignment matrix; after this step a cyclic block model is applied, subdividing each part equally between all available nodes .TP \fB\-H\fR (mpialign only) number of horizontal subdivisions made by each node to its alignment submatrix; since this value defines block width, a good choice should allow two full matrix lines to fit the processor's cache pages, improving algorithm performance .TP \fB\-V\fR (mpialign only) number of vertical subdivisions made by each node to its alignment submatrix; this value directly affects the amount of internode communication and is used ONLY if 'split' is set to 1, otherwise it is set to the number of available nodes debian/docs0000664000000000000000000000001412016702075010036 0ustar NEWS README debian/patches/0000775000000000000000000000000012100005212010576 5ustar debian/patches/series0000664000000000000000000000002012100004472012012 0ustar hardening.patch debian/patches/hardening.patch0000664000000000000000000000131612100005212013557 0ustar Author: Andreas Tille LastChanged: Wed, 23 Jan 2013 17:04:13 +0100 Description: Try hard to get CXXFLAGS into build to enable hardening CXXFLAGS are hardwired inside configure.in so simply setting the environment variable does not help here and we need to recreate configure script using dh_autoreconf --- a/configure.in +++ b/configure.in @@ -33,7 +33,7 @@ ACX_MPI # Set compiler and compiler flags CXX="$MPICXX" CFLAGS="-g -O0" -CXXFLAGS="-g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm" +CXXFLAGS="-g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm ${CXXFLAGS}" # Autoconf output AC_CONFIG_FILES([