debian/0000755000000000000000000000000012265171550007172 5ustar debian/control0000644000000000000000000000771612265007106010603 0ustar Source: mrbayes Maintainer: Debian Med Packaging Team Uploaders: Fernando Ribeiro , Steffen Moeller , Dominique Belhachemi , Pjotr Prins , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), libreadline-dev, mpi-default-dev, libhmsbeagle-dev (<< 2.1-1) | libhmsbeagle-dev (>= 2.1-2), autoconf, automake Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/mrbayes/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mrbayes/trunk/ Homepage: http://mrbayes.csit.fsu.edu/ Package: mrbayes Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libhmsbeagle1 Suggests: mrbayes-doc Description: Bayesian Inference of Phylogeny Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. Package: mrbayes-mpi Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, mpi-default-bin Suggests: mpi-default, mrbayes-doc Description: Bayesian Inference of Phylogeny - mpi version Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. . This package offers a binary compiled for parallel computation with MPI. Package: mrbayes-dbg Architecture: any Section: debug Priority: extra Depends: ${misc:Depends}, mrbayes (= ${binary:Version}) | mrbayes-mpi (= ${binary:Version}) Breaks: mrbayes (<< ${binary:Version}), mrbayes (>> ${binary:Version}), mrbayes-mpi (<< ${binary:Version}), mrbayes-mpi (>> ${binary:Version}) Description: Bayesian Inference of Phylogeny - debug symbols Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. . The package provides the debug symbols that are otherwise stripped from the binaries to reduce the footprint of the package. This package can be installed to help debugging of problems when running mrbayes. Package: mrbayes-doc Architecture: all Section: doc Priority: extra Depends: ${misc:Depends} Enhances: mrbayes Description: Bayesian Inference of Phylogeny - manual Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. . This package provides the manual for MrBayes. debian/mb-mpi0000644000000000000000000000024212214301010010250 0ustar #!/bin/sh # To use more than one processor set MPI_OPTIONS - eg. # # export MPI_OPTIONS="-np 4" exec mpirun `echo $MPI_OPTIONS` /usr/lib/mrbayes-mpi/mb-mpi "$@" debian/mrbayes-doc.install0000644000000000000000000000006012214301010012737 0ustar documentation/Manual*.pdf usr/share/doc/mrbayes debian/mrbayes-mpi.README.Debian0000644000000000000000000000053412214301010013435 0ustar MrBayes for Debian ------------------ This is the MPI version of MrBayes. You can download the Manual for MrBayes as PDF from http://mrbayes.sourceforge.net/mb3.1_manual.pdf The command reference can be downloaded here http://mrbayes.sourceforge.net/commref_mb3.1.pdf -- Andreas Tille Thu, 03 Feb 2011 22:23:31 +0100 debian/rules0000755000000000000000000000200512265000657010246 0ustar #!/usr/bin/make -f # debian/rules for mrbayes # Andreas Tille # GPL # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ --sourcedirectory=src override_dh_auto_configure: #Configure for MPI at first ( cd src ; autoconf ) dh_auto_configure -- --with-beagle=/usr --enable-mpi=yes --enable-debug=yes override_dh_auto_clean: ( cd src ; $(MAKE) -f Makefile.in distclean ) rm -f src/configure rm -f mb mb-mpi src/mb override_dh_auto_build: # build mb-mpi (from initial config) LIBS="-Wl,--as-needed" dh_auto_build mv src/mb ./mb-mpi # Now - build mb ( cd src ; make clean ) dh_auto_configure -- --with-beagle=/usr --enable-mpi=no --enable-debug=yes LIBS="-Wl,--as-needed" dh_auto_build mv src/mb . override_dh_auto_install: echo "Do not try to install to /usr/local/bin" override_dh_strip: dh_strip --dbg-package=mrbayes-dbg override_dh_compress: dh_compress --exclude=.pdf override_dh_builddeb: dh_builddeb -- -Z xz get-orig-source: uscan --verbose --force-download debian/mb-mpi.10000644000000000000000000000047412214301010010416 0ustar .TH mrbayes "1" "Nov 2006" "mrbayes 3.1.2" "User Commands" .SH NAME mb-mpi \- A program for the Bayesian estimation (parallel version) .SH SYNOPSIS .B mb-mpi [OPTION]... [FILE]... .SH DESCRIPTION A program for the Bayesian estimation of phylogeny Bayesian inference of phylogeny .SH OPTIONS .B \-i interactive mode debian/watch0000644000000000000000000000020012214301010010167 0ustar version=3 opts=dversionmangle=s/\+dfsg// \ http://sf.net/mrbayes/mrbayes-([\d\.]+)\.tar\.gz \ debian debian/get-orig-source debian/mrbayes-mpi.install0000644000000000000000000000006212214301010012761 0ustar mb-mpi usr/lib/mrbayes-mpi debian/mb-mpi usr/bin debian/mrbayes-mpi.manpages0000644000000000000000000000002012214301010013100 0ustar debian/mb-mpi.1 debian/upstream0000644000000000000000000000265412214301010010740 0ustar Reference: - Author: Fredrik Ronquist and Maxim Teslenko and Paul van der Mark and Daniel L. Ayres and Aaron Darling and Sebastian Höhna and Bret Larget and Liang Liu and Marc A. Suchard and John P. Huelsenbeck Title: "MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space" Journal: Systematic Biology Year: 2012 DOI: 10.1093/sysbio/sys029 PMID: 22357727 URL: http://sysbio.oxfordjournals.org/content/early/2012/03/02/sysbio.sys029.abstract eprint: http://sysbio.oxfordjournals.org/content/early/2012/03/02/sysbio.sys029.full.pdf+html - Author: Fredrik Ronquist and John P. Huelsenbeck Title: "MrBayes 3: Bayesian phylogenetic inference under mixed models" Journal: Bioinformatics Year: 2003 Volume: 19 Number: 12 Pages: 1572-1574 DOI: 10.1093/bioinformatics/btg180 PMID: 12912839 URL: http://bioinformatics.oxfordjournals.org/content/19/12/1572.abstract eprint: http://bioinformatics.oxfordjournals.org/content/19/12/1572.full.pdf+html - Author: John P. Huelsenbeck and Fredrik Ronquist Title: "MRBAYES: Bayesian inference of phylogenetic trees" Journal: Bioinformatics Year: 2001 Volume: 17 Number: 8 Pages: 754-755 DOI: 10.1093/bioinformatics/17.8.754 PMID: 11524383 URL: http://bioinformatics.oxfordjournals.org/content/17/8/754.abstract eprint: http://bioinformatics.oxfordjournals.org/content/17/8/754.full.pdf+html debian/copyright0000644000000000000000000000271212214301010011103 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: MrBayes Upstream-Contact: Fredrik Ronquist Source: http://mrbayes.sourceforge.net/ Files: * Copyright: © 2002-2012 Fredrik Ronquist , John Huelsenbeck , Paul van der Mark , Bred Larget, Donald Simon. License: GPL-2+ Files: debian/* Copyright: © 2006 Fernando Ribeiro © 2011-2012 Andreas Tille License: GPL-2+ License: GPL-2+ 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 2 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 2 can be found in the file `/usr/share/common-licenses/GPL-2'. debian/mrbayes.README.Debian0000644000000000000000000000046712214301010012657 0ustar MrBayes for Debian ------------------ You can download the Manual for MrBayes as PDF from http://mrbayes.sourceforge.net/mb3.1_manual.pdf The command reference can be downloaded here http://mrbayes.sourceforge.net/commref_mb3.1.pdf -- Andreas Tille Thu, 03 Feb 2011 22:23:31 +0100 debian/source/0000755000000000000000000000000011522615464010474 5ustar debian/source/format0000644000000000000000000000001411467561373011711 0ustar 3.0 (quilt) debian/get-orig-source0000755000000000000000000000246712264765421012151 0ustar #!/bin/sh # get source for mrbayes to obtain documentation source from SVN set -e # set -x NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` COMPRESSION=xz if ! echo $@ | grep -q upstream-version ; then VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` # regard dversionmangle VERSION=`echo ${VERSION} | sed 's/\([0-9]\)~\([br]\)/\1-\2/'` else VERSION=`echo $@ | sed "s?^.*--upstream-version \([-0-9.rcbeta]\+\) .*${NAME}.*?\1?"` if echo "$VERSION" | grep -q "upstream-version" ; then echo "Unable to parse version number" exit fi fi mkdir -p ../tarballs cd ../tarballs TARDIR=${NAME}_${VERSION} mv ../${NAME}-${VERSION}.tar.gz . tar -xzf ${NAME}-${VERSION}.tar.gz # remove PDF without source rm -f ${TARDIR}/documentation/commref*.pdf # fetch sources for remaining doc from SVN into temporary dir svn export https://svn.code.sf.net/p/mrbayes/code/documentation tmp # remove unneeded stuff from documentation SVN rm -f tmp/Manual*.pdf rm -f tmp/*.rtf rm -f tmp/*.rb rm -f tmp/Release_instructions.txt # move remaining doc to source dir mv tmp/* ${TARDIR}/documentation rmdir tmp GZIP="--best --no-name" XZ_OPT="-6v" tar --owner=root --group=root --mode=a+rX -a -cf ${TARDIR}+dfsg.orig.tar.${COMPRESSION} ${TARDIR} rm -rf ${TARDIR} debian/mb.10000644000000000000000000000044112214301010007625 0ustar .TH mrbayes "1" "Nov 2006" "mrbayes 3.1.2" "User Commands" .SH NAME mb \- A program for the Bayesian estimation .SH SYNOPSIS .B mb [OPTION]... [FILE]... .SH DESCRIPTION A program for the Bayesian estimation of phylogeny Bayesian inference of phylogeny .SH OPTIONS .B \-i interactive mode debian/mrbayes.manpages0000644000000000000000000000001412214301010012320 0ustar debian/mb.1 debian/changelog0000644000000000000000000000766412265171453011063 0ustar mrbayes (3.2.2+dfsg-1) unstable; urgency=medium * New upstream version * debian/control: - cme fix dpkg-control Remark: Pre-Depends: dpkg (>= 1.15.6~) can definitely be dropped since even oldstable has a later dpkg. Most probably a very old lintian was used in the check for the previous version - Canoncial Vcs fields - mrbayes-dbg: s/Conflicts/Breaks/ - Build-Depends: libhmsbeagle-dev (<< 2.1-1) | libhmsbeagle-dev (>= 2.1-2) since libhmsbeagle-dev (= 2.1-1) is lacking the unversioned header dir * debian/patches/ldlibs.patch: Make sure we are properly linking against all libs * debian/rules: deactivate dh_auto_install since it tries to move files to /usr/local/bin * debian/README.source: removed since redundant -- Andreas Tille Mon, 13 Jan 2014 14:38:47 +0100 mrbayes (3.2.1+dfsg-2ubuntu1) precise; urgency=low * Rebuild for Ubuntu. Fix Lintian warning about xz -- Tim Booth Fri, 10 Aug 2012 15:58:14 +0100 mrbayes (3.2.1+dfsg-2) unstable; urgency=low [ Andreas Tille ] * debian/upstream: Add publication data * debian/patches/as-needed.patch: Enable building using --as-needed thanks for the patch to Ilya Barygin Closes: #678175 * debian/control: Dropped quilt from Build-Depends * debhelper 9 (control+compat) * debian/rules: use xz compression [ Charles Plessy ] * debian/control: corrected a typo (Closes: #671666). -- Andreas Tille Fri, 10 Aug 2012 15:37:50 +0200 mrbayes (3.2.1+dfsg-1) unstable; urgency=low * New upstream version * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs fields * debian/control: Fixed DEP5 issues and verified using cme fix dpkg-copyright -- Andreas Tille Tue, 03 Apr 2012 09:13:36 +0200 mrbayes (3.2.0+dfsg-1) unstable; urgency=low * New upstream version uploaded to Debian * debian/patches: removed because applied upstream * debian/control: - ehanced description of mrbayes-dbg - added doc package featuring the provided manual * debian/watch: call debian/get-orig-source to fetch sources for PDF documentation * debian/get-orig-source: Create new tarball including source for PDF documentation. * debian/rules: - get-orig-source target - prevent dh_compress from compressing docs * debian/mrbayes-doc.install: install documentation * debian/mrbayes-doc.doc-base -- Andreas Tille Sat, 21 Jan 2012 21:07:23 +0100 mrbayes (3.2.0-2) lucid; urgency=low * A couple of build fixes * Add dependencies on autotools * Now builds against Beagle library so CUDA should be possible -- Tim Booth Wed, 14 Dec 2011 13:05:36 +0000 mrbayes (3.2.0-1) lucid; urgency=low * Rebuild of new 3.2.0 release. Pjotr mentioned having a package for the pre-release but I can't find that work in SVN. * Current build is without Beagle - this needs packaging - nothing to do with existing libbeagle-dev package. -- Tim Booth Tue, 06 Dec 2011 16:57:45 +0000 mrbayes (3.1.2-3) UNRELEASED; urgency=low * Added -dbg package. -- Steffen Moeller Wed, 12 Oct 2011 21:36:05 +0200 mrbayes (3.1.2-2) unstable; urgency=low * debian/control: - Depends: s/openmpi-common, openmpi-bin/mpi-default-bin/ Closes: #630994 - Standards-Version: 3.9.2 (no changes needed) * Debhelper 8 (control+compat) -- Andreas Tille Wed, 29 Jun 2011 16:02:55 +0200 mrbayes (3.1.2-1) unstable; urgency=low * Initial release in Debian (Closes: #611928) -- Andreas Tille Thu, 03 Feb 2011 22:23:31 +0100 mrbayes (3.1.2-0ubuntu1) feisty; urgency=low * Initial release. * Patch applied: misc/makefile_clean_binary.diff * Patch applied: misc/man1.diff -- Fernando Ribeiro Thu, 9 Nov 2006 02:37:20 -0200 debian/patches/0000755000000000000000000000000012265006031010610 5ustar debian/patches/as-needed.patch0000644000000000000000000000100012264766216013466 0ustar Description: fix FTBFS with --as-needed linker option This way, libraries will be added to ld call after object files. Author: Ilya Barygin Bug-Debian: http://bugs.debian.org/678175 Last-Changed: Tue, 19 Jun 2012 19:03:09 UTC --- a/src/Makefile.in +++ b/src/Makefile.in @@ -2,7 +2,7 @@ srcdir = @srcdir@ RM = rm CC = @CC@ CFLAGS = @CFLAGS@ -DUSECONFIG_H -LDFLAGS = @LDFLAGS@ -lm +LDLIBS = @LDFLAGS@ -lm INSTALL = @INSTALL@ BINDIR = /usr/local/bin debian/patches/ldlibs.patch0000644000000000000000000000061512264771160013117 0ustar Author: Andreas Tille Last-Update: Mon, 13 Jan 2014 14:38:47 +0100 Description: Make sure we are properly linking against all libs --- a/src/Makefile.in +++ b/src/Makefile.in @@ -13,7 +13,7 @@ PROGS = mb all: $(PROGS) mb: $(OBJECTS) - $(CC) $(CFLAGS) -o $@ $^ $(LDFLAGS) + $(CC) $(CFLAGS) -o $@ $^ $(LDLIBS) install: $(PROGS) $(INSTALL) -m 755 $(PROGS) $(BINDIR) debian/patches/series0000644000000000000000000000006612265006031012027 0ustar as-needed.patch ldlibs.patch # new_libhmsbeagle.patch debian/patches/new_libhmsbeagle.patch0000644000000000000000000000000012265005452015114 0ustar debian/mrbayes.install0000644000000000000000000000001312214301010012172 0ustar mb usr/bin debian/compat0000644000000000000000000000000212214301010010344 0ustar 9 debian/mrbayes-doc.doc-base0000644000000000000000000000137512214301010012760 0ustar Document: mrbayes-doc Title: MrBayes version 3.2 Manual: Tutorials and Model Summaries Author: Fredrik Ronquist, John Huelsenbeck and Maxim Teslenko Abstract: Bayesian Inference of Phylogeny Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. Section: Science/Biology Format: pdf Files: /usr/share/doc/mrbayes/Manual_MrBayes_v3.2.0_draft.pdf