debian/0000775000000000000000000000000012253243161007167 5ustar debian/rules0000775000000000000000000000012111723655417010255 0ustar #!/usr/bin/make -f %: dh $@ override_dh_clean: dh_clean rm -rf clustalw-mpi debian/changelog0000664000000000000000000001074612253243161011051 0ustar clustalw-mpi (0.15-3build1) trusty; urgency=medium * No-change rebuild for libopenmpi1.3 -> libopenmpi1.6 transition. -- Logan Rosen Sun, 15 Dec 2013 01:04:18 -0500 clustalw-mpi (0.15-3) unstable; urgency=low * Removed obsolete DM-Upload-Allowed field. * Using Debhelper 9. * Normalised VCS URLs. * Normalised debian/control using config-model. * Conforms to Policy 3.9.4. * Version link to GPL-2 in debian/copyright. * Escape minus sign in ‘debian/clustalw-mpi.1’. * Uploaded for openmpi transition (Closes: #722073). -- Charles Plessy Sun, 08 Sep 2013 10:08:06 +0900 clustalw-mpi (0.15-2) unstable; urgency=low * debian/control: - Fixed Vcs-Fields - Updated Standards-Version to 3.9.3 (no changes needed) - Homepage has changed - Build-Depends: mpi-default-dev Closes: #661740 - Depends ${misc:Depends} - Dropped Build-Depends: cdbs * debian/source/format: 3.0 (quilt) * Debhelper compat level 8 (control+compat) * debian/copyright: Fixed DEP5 issues using cme fix dpkg-copyright * deleted debian/README.Debian because there is no point in just using different words for a package beeing in non-free as it is just said in debian/copyright * debian/watch: Deleted because not working * debian/rules: - Delete get-orig-source target because not working any more because source vanished - Rewritten using dh * debian/upstream: bibliographic information * debian/README.source: document missing source code for current version -- Andreas Tille Thu, 01 Mar 2012 12:16:54 +0100 clustalw-mpi (0.15-1) unstable; urgency=low * New upstream release. - Fixes crash when the length of a sequence's name was longer than 60 characters. You must re-define macro MAXNAMES in order to process FASTA file with sequence names longer than the default length. * Updated my email address. * Updated upstreams' email address. * Refreshed the manpage. * debian/copyright: - Lifted debian/copyright to the latest version, and licenced my contribution to this packaging work to "Same as CLUSTALW-MPI". - Added a disclaimer clarifying that this package is not part of the Debian operating system (requirement of Policy 3.8.0). * debian/patches/01_Makefile.patch removed. Its function is now carried out by debian/rules and debhelper. * debian/rules switched to CDBS. * debian/control: - Dropped build-dependancy on quilt and added one on cdbs. - Updated Standards-Version to 3.8.0. -- Charles Plessy Sat, 05 Jul 2008 17:22:23 +0900 clustalw-mpi (0.14-1) unstable; urgency=low [ Andreas Tille ] * Put package under group maintenance of Debian-Med Team - DM-Upload-Allowed: Yes - Vcs tags - Use correct address as Uploader: Steffen Moeller * Switched to quilt - Move manpage to debian dir and added debian/manpages - Patched Makefile accordingly - removed useless t.sh * Standards-Version: 3.7.3 (no changes needed) * debhelper >= 5 * Moved Homepage from long description to control fields * debian/copyright machine readable * Removed [Biology] from short description [ Charles Plessy ] * Bug fix version 0.14 released on Dec 19, 2005. See /usr/share/doc/clustalw-mpi/History for more details. * Updated debian/patches for the new upstream version. * Added myself to the Hall of Fame of debian/copyright and to the Uploaders in debian/control. * Updated homepage in debian/copyright and debian/control. * Added debian/watch file. * debian/clustalw-mpi.1: incremented version number. * debian/control: - Dropped versioned dependencies on lam packages, as they are satisfied even in Sarge. - Updated homepage of Clustal. -- Andreas Tille Sun, 06 Apr 2008 20:23:04 +0200 clustalw-mpi (0.13-3) unstable; urgency=low * Updated lam4 to 7.1.1 (Closes: Bug#329488) -- Steffen Moeller Wed, 12 Oct 2005 15:07:41 +0200 clustalw-mpi (0.13-2) unstable; urgency=low * Updated lam3 to lam4 (Closes: #229939) -- Steffen Moeller Mon, 30 Jun 2003 22:54:41 +0200 clustalw-mpi (0.13-1) unstable; urgency=low * Initial Release. (Closes: #199837) * Upstream author was very supportive - provided man page - provided license information * Minimal changes to the makefile -- Steffen Moeller Mon, 30 Jun 2003 22:54:41 +0200 debian/upstream0000664000000000000000000000072711723654064010771 0ustar Contact: Dr. Kuo-Bin Li Name: ClustalW-MPI Homepage: http://www.bii.a-star.edu.sg/achievements/applications/clustalw/ Remark: The source is only available in a previous version (0.13) at the homepage Reference: author: Kuo-Bin Li title: "ClustalW-MPI: ClustalW Analysis Using Distributed and Parallel Computing" journal: Bioinformatics volume: 19 number: 12 pages: 1585-1586 year: 2003 DOI: 10.1093/bioinformatics/btg192 PMID: 12912844 debian/compat0000664000000000000000000000000212212735216010367 0ustar 9 debian/README.source0000664000000000000000000000063411723654514011362 0ustar ClustalW-MPI for Debian ----------------------- This source was originally downloaded from http://kmlvli.com/kuobin/clustalw-mpi/clustalw-mpi-0.15.tar.gz but the host kmlvli.com seems to have vanished. The homepage of ClustalW-MPI just contains a previous version (0.13). Feel free to contact the upstream author for clarification. -- Andreas Tille Thu, 01 Mar 2012 11:41:19 +0100 debian/copyright0000664000000000000000000000355712212741354011136 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: ClustalW-MPI Upstream-Contact: Dr. Kuo-Bin Li Source: http://kmlvli.com/kuobin/clustalw-mpi/clustalw-mpi-0.15.tar.gz Remark: The download host vanished and the new homepage does only contain a previous version 0.13 Disclamer: This package is not part of the Debian operating system. The clustalw-mpi source and binary Debian packages are part of the "non-free" area in our archive. The packages in this area are not part of the Debian system, although they have been configured for use with Debian. We nevertheless support the use of the clustalw-mpi source and binary Debian packages by providing infrastructure such as our bug tracking system and mailing lists. Files: * Copyright: © 2001-2008 Dr. Kuo-Bin Li, Bioinformatics Institute, Singapore License: derived_from_clustal_w CLUSTALW-MPI is freely available to the user community. You can redistribute it and/or modify it. Since CLUSTALW-MPI was derived from CLUSTAL W, the original license policy of CLUSTAL W is listed here: . Clustal W is freely available to the user community. However, Clustal W is increasingly being distributed as part of commercial sequence analysis packages. To help us safeguard future maintenance and development, commercial distributors of Clustal W must take out a NON-EXCLUSIVE LICENCE. Anyone wishing to commercially distribute version 1.81 of Clustal W should contact the authors unless they have previously taken out a licence. Files: debian/* Copyright: © 2003—2008 Steffen Moeller © 2008 Charles Plessy © 2003—2012 Andreas Tille License: GPL-2+ On Debian systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'. debian/source/0000775000000000000000000000000012212746776010506 5ustar debian/source/format0000664000000000000000000000001411723647225011707 0ustar 3.0 (quilt) debian/manpages0000664000000000000000000000002610776337444010723 0ustar debian/clustalw-mpi.1 debian/clustalw-mpi.10000664000000000000000000000226112212742703011674 0ustar .\" .\" The man page was derived from the man page of Chet Ramey for the BASH .\" .TH CLUSTALW\-MPI 1 "2008\ June\ 3" "ClustalW\-MPI 0.15" .SH NAME ClustalW-MPI \- MPI distributed ClustalW .SH SYNOPSIS mpirun [\fImpirun_options\fR] clustalw-mpi [\fIclustalw options\fR] .SH DESCRIPTION .B ClustalW-MPI is an MPI implementation of ClustalW. It utilizes your networked computers to globally align sets of nucleic or amino acid sequences. .SH EXAMPLES To make a full multiple sequence alignment (using one master node and 4 computing nodes): mpirun \-np 5 ./clustalw-mpi \-infile=dele.input To make a guide tree only: mpirun \-np 5 ./clustalw-mpi \-infile=dele.input \-newtree=dele.mytree To make a multiple sequence alignment out of an existing tree: mpirun \-np 5 ./clustalw-mpi \-infile=dele.input \-usetree=dele.mytree .SH COPYRIGHT .if n clutalw-mpi is Copyright (C) 2003 by Dr. Kuo-Bin Li, Bioinformatics Institute, Singapure .if t clutalw-mpi is Copyright \(co 2003 by Dr. Kuo-Bin Li, Bioinformatics Institute, Singapure .SH OPTIONS See man page for clustalw. .SH SEE ALSO .B clustalw (1) .SH AUTHORS Dr. Kuo-Bin Li , Bioinformatics Institute, Singapore. debian/install0000664000000000000000000000002511033631002010543 0ustar clustalw-mpi usr/bin debian/examples0000664000000000000000000000002611033432457010731 0ustar db10.input dele.input debian/control0000664000000000000000000000411512212736061010574 0ustar Source: clustalw-mpi Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Charles Plessy Section: non-free/science Priority: optional Build-Depends: debhelper (>= 9), mpi-default-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/clustalw-mpi/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/clustalw-mpi/trunk/ Homepage: http://www.bii.a-star.edu.sg/achievements/applications/clustalw/ XS-Autobuild: yes Package: clustalw-mpi Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: seaview, clustalx Enhances: clustalw Description: MPI-distributed global sequence alignment with ClustalW ClustalW is a popular tool for multiple sequence alignment. The alignment is achieved via three steps: pairwise alignment, guide-tree generation and progressive alignment. ClustalW-MPI is an MPI implementation of ClustalW. Based on version 1.82 of the original ClustalW, both the pairwise and progressive alignments are parallelized with MPI, a popular message passing programming standard. The pairwise alignments can be easily parallelized since the many alignments are time independent on each other. However the progressive alignments are essentially not parallelizable because of the time dependencies between each alignment. . Here the recursive parallelism paradigm is applied to the linear space profile-profile alignment algorithm. This approach is more time efficient on computers with distributed memory architecture. Traditional approach that relies on precomputing the profile-profile score matrix has also been implemented. Results shown the latter is indeed more appropriate for shared memory multiprocessor computer. . ClustalX is suggested for its support for local realignments, seaview is a versatile editor of alignments. . The original ClustalW/ClustalX can be found at URL: http://www.clustal.org/download/pre-2/ debian/docs0000664000000000000000000000003411033432457010042 0ustar README.clustalw-mpi History