debian/0000755000000000000000000000000012151652445007173 5ustar debian/control0000644000000000000000000001074512112223633010573 0ustar Source: beast-mcmc Section: contrib/science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Andreas Tille , Olivier Sallou Build-Depends: debhelper (>= 9), javahelper (>=0.25), ant, ant-optional, default-jdk, libjebl2-java, libjam-java, figtree, liboptions-java, libhmsbeagle-java (>= 1.1r1092), libcolt-java, libmpj-java, r-cran-rjava, libcommons-math-java (>= 2.2), libjdom1-java, junit4, libmtj-java, libitext1-java, texlive-latex-base, texlive-latex-extra Standards-Version: 3.9.4 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/beast-mcmc/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/beast-mcmc/trunk/ XS-Autobuild: yes Homepage: http://beast.bio.ed.ac.uk/ Package: beast-mcmc Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, libhmsbeagle-java (>= 1.1r1092), ${java:Depends}, default-jre | java6-runtime, libnucleotidelikelihoodcore0 (>= ${source:Version}) Suggests: beast-mcmc-doc Description: Bayesian MCMC phylogenetic inference BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Included is a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. Package: libnucleotidelikelihoodcore0 Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Replaces: beast-mcmc-lib Conflicts: beast-mcmc-lib Provides: beast-mcmc-lib Section: contrib/libs Description: implementation of LikelihoodCore for nucleotides used by beast-mcmc BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Included is a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. . This package an implementation of LikelihoodCore for nucleotides that calls native methods for maximum speed. Package: beast-mcmc-examples Architecture: all Section: contrib/doc Depends: ${shlibs:Depends}, ${misc:Depends} Enhances: beast-mcmc Description: Bayesian MCMC phylogenetic inference - example data BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Included is a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. . This package contains the example data. Package: beast-mcmc-doc Architecture: all Section: contrib/doc Depends: ${shlibs:Depends}, ${misc:Depends} Enhances: beast-mcmc Description: Bayesian MCMC phylogenetic inference - documentation BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Included is a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. . This package contains the documentation. debian/beast-mcmc.10000755000000000000000000001224611400665731011276 0ustar .\" Title: BEAST-MCMC .\" Author: Alexei J. Drummond .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: 05/28/2010 .\" Manual: BEAST-MCMC Manual .\" Source: BEAST 1.5.3 .\" .TH "BEAST\-MCMC" "1" "05/28/2010" "BEAST 1.5.3" "BEAST-MCMC Manual" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" beast-mcmc \- Bayesian evolutionary analysis sampling trees .SH "SYNOPSIS" .HP 11 \fBbeast\-mcmc\fR [\fBOPTIONS\fR] [\fIinput\&.xml\fR] .HP 11 \fBbeast\-mcmc\fR [\fB\-verbose\fR | \fB\-strict\fR | \fB\-window\fR | \fB\-options\fR | \fB\-working\fR | \fB\-seed\fR | \fB\-errors\ i\fR | \fB\-threads\ i\fR | \fB\-java\fR | \fB\-beagle\fR | \fB\-beagle_info\fR | \fB\-beagle_resource_order\fR | \fB\-help\fR | \fBinput\&.xml\fR] .SH "DESCRIPTION" .PP BEAST is a cross\-platform program for Bayesian MCMC analysis of molecular sequences\&. It is orientated towards rooted, time\-measured phylogenies inferred using strict or relaxed molecular clock models\&. It is intended both as a method of reconstructing phylogenies and as a framework for testing evolutionary hypotheses without conditioning on a single tree topology\&. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability\&. We include a simple to use user\-interface program for setting up standard analyses and a suite of programs for analysing the results\&. There are three main areas of research for which the BEAUti/BEAST package is particularly applicable\&. These areas are species phylogenies for molecular dating, coalescent\-based population genetics and measurably evolving populations (ancient DNA or time\-stamped viral sequence data sets)\&. .SH "OPTIONS" .PP \fB\-verbose\fR .RS 4 verbose XML parsing messages .RE .PP \fB\-strict\fR .RS 4 fail on non conforming BEAST XML file .RE .PP \fB\-window\fR .RS 4 provide a console window .RE .PP \fB\-options\fR .RS 4 display an options dialog .RE .PP \fB\-working\fR .RS 4 change working directory to input file\'s directory .RE .PP \fB\-seed\fR .RS 4 specify a random number generator seed .RE .PP \fB\-errors \fR\fB\fIi\fR\fR .RS 4 maximum number of numerical errors before stopping .RE .PP \fB\-threads \fR\fB\fIi\fR\fR .RS 4 the number of computational threads to use (default 1) .RE .PP \fB\-java\fR .RS 4 use Java only, no native implementations .RE .PP \fB\-beagle\fR .RS 4 use beagle library if available .RE .PP \fB\-beagle_info\fR .RS 4 show information on available beagle resources .RE .PP \fB\-beagle_resource_order\fR .RS 4 set order of beagle resources .RE .PP \fB\-help\fR .RS 4 print usage screen .RE .SH "BUGS" .PP The BEAST bug tracking system can be found at \fI\%http://code.google.com/p/beast-mcmc/issues/list\fR\&. .SH "SEE ALSO" .PP \fBbeauti\fR(1)\&. .SH "REFERENCES" .sp .RS 4 \h'-04'\(bu\h'+03'Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees\&." BMC Evolutionary Biology 7:214\&. .RE .sp .RS 4 \h'-04'\(bu\h'+03'Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88\&. .RE .sp .RS 4 \h'-04'\(bu\h'+03'Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185\-1192\&. .RE .sp .RS 4 \h'-04'\(bu\h'+03'Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307\-1320\&. .RE .SH "AUTHORS" .PP \fBAlexei J\&. Drummond\fR .sp -1n .IP "" 4 Copyright holder for BEAST\&. .PP \fBAndrew Rambaut\fR .sp -1n .IP "" 4 Copyright holder for BEAST\&. .PP \fBMarc A\&. Suchard\fR .sp -1n .IP "" 4 Copyright holder for BEAST\&. .PP \fBFelix Feyertag\fR <\&felix\&.feyertag@googlemail\&.com\&> .sp -1n .IP "" 4 Prepared this manpage in DocBook XML for the Debian distribution\&. .SH "COPYRIGHT" Copyright \(co 2002\(en2010 Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard (BEAST) .br Copyright \(co 2009\(en2010 Felix Feyertag (This manpage) .br .PP The binaries and source code are made available and can be distributed subject to the following conditions: .PP BEAST is Copyright (C) 2002\-2006 Alexei Drummond and Andrew Rambaut BEAST is distributed under the terms of the GNU Lesser General Public License\&. See the notice in individual files and the file LICENSE for licensing details\&. .PP BEAST includes software libraries from projects whose licensing terms require that the following notices be included when they are distributed in binary form and that the recipient be given a copy of their respective licenses\&. .sp .RS 4 \h'-04'\(bu\h'+03'This product includes software developed by the JDOM Project (http://www\&.jdom\&.org/) .RE .sp .RS 4 \h'-04'\(bu\h'+03'This product includes software developed by The Apache Software Foundation (http://www\&.apache\&.org/) .RE .sp .RS 4 \h'-04'\(bu\h'+03'The license for JDOM can be read in the LICENSE\&.txt file in the source distribution available at http://www\&.jdom\&.org/ .RE .sp .RS 4 \h'-04'\(bu\h'+03'The license for the Commons Math library can be read at http://www\&.apache\&.org/licenses/LICENSE\-2\&.0 or in the LICENSE\&.txt file in the source distribution available at http://jakarta\&.apache\&.org/commons/math/ .RE .PP This manual page and its XML source can be used, modified, and redistributed as if it were in public domain\&. .sp debian/tracer0000644000000000000000000000060111703306003010357 0ustar #!/bin/sh echo "dr/app/tracer/application/TracerApp is missing in beast.jar - build system needs fixing!" exit 1 BEAST_LIB="/usr/share/beast-mcmc" DEBJAR="/usr/share/java" java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \ -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \ dr/app/tracer/application/TracerApp $* debian/README.source0000644000000000000000000000020112151645640011342 0ustar There is a new upstream release with major changes which most probably need a lot of packaging changes which has not yet started debian/beauti.xpm0000644000000000000000000001306611523176354011202 0ustar /* XPM */ static char *beauti_[] = { /* columns rows colors chars-per-pixel */ "32 32 155 2", " c #3631362F362E", ". c #560A55C85596", "X c #5AC35AC55AC5", "o c #7ED87E837E6A", "O c #39919FC5DFCC", "+ c #2F689BF9E262", "@ c #2E10A265E76A", "# c #3CE8A304E4A4", "$ c #3EBBA676E8A6", "% c #33FAAD5CEE5F", "& c #3BF8AB9FEC47", "* c #7E3DB440D034", "= c #74A6AFA0D4CE", "- c #76D5B285D632", "; c #727CB3CFDC0A", ": c #724EB911E03F", "> c #42B5A5D2E588", ", c #47CAA827E65B", "< c #49FEA94DE6A3", "1 c #4D2BAECAE9CA", "2 c #52D9AD14E72A", "3 c #44DBBD99EBAE", "4 c #59AFB186E9B0", "5 c #50D8B83AF076", "6 c #5EF6BF28F241", "7 c #61FCB3D6E67F", "8 c #6565B8F0E3BF", "9 c #6368B566EA27", "0 c #6ED9BAE4EBDD", "q c #7B17BC62E397", "w c #759ABE07EC97", "e c #7A1DBF39EB86", "r c #4CEAC538ED99", "t c #5EE1C5AEE658", "y c #55F4C204ED26", "u c #5202C5AAF2E5", "i c #59B9C202F0BA", "p c #64A6C23CE638", "a c #6BFEC5DEE3A0", "s c #6C94C89BED10", "d c #6FF2C06DE3F8", "f c #74BDCA4FE7E1", "g c #7EB2C27BEDCB", "h c #7DEECD7CEC29", "j c #69AFC8A6F10A", "k c #7907C566F36B", "l c #83EC83908363", "z c #89E189698923", "x c #95939541952F", "c c #9C719C5A9C55", "v c #A006A012A034", "b c #9F25B3ABBDE1", "n c #A4B3A48BA46E", "m c #AB4CAB29AB04", "M c #B033B01DB024", "N c #AD2AB2D7B5D8", "B c #A274B4C0BF95", "V c #B5D3B589B568", "C c #B8CFB7EFB7CE", "Z c #B8F5B849B77D", "A c #B47CBD49BE50", "S c #BBE1BBBCBBA4", "D c #8445B364CC4F", "F c #8BD0B5D9CD03", "G c #93FBB5C2C3E7", "H c #91D1B615CC42", "J c #93A0B898CF5A", "K c #9C56B8DEC880", "L c #802DB44BD10C", "P c #897FB771D1DD", "I c #8E08BDAFD6E9", "U c #87C9BE16DCFB", "Y c #A163BB22CB55", "T c #B82CBFE2C42C", "R c #BD65BFAAC08C", "E c #9F9DC40CCE40", "W c #8661C142E004", "Q c #9DCAC465D2C9", "! 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Drummond Copyright holder for &dhproduct;. Andrew Rambaut Copyright holder for &dhproduct;. Marc A. Suchard Copyright holder for &dhproduct;. &dhfirstname; &dhsurname; Prepared this manpage in DocBook XML for the Debian distribution.
&dhemail;
2002–2009 Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard (&dhproduct;) 2002–2009 &dhusername; (This manpage) The binaries and source code are made available and can be distributed subject to the following conditions: BEAST is Copyright (C) 2002-2006 Alexei Drummond and Andrew Rambaut BEAST is distributed under the terms of the GNU Lesser General Public License. See the notice in individual files and the file LICENSE for licensing details. BEAST includes software libraries from projects whose licensing terms require that the following notices be included when they are distributed in binary form and that the recipient be given a copy of their respective licenses. This product includes software developed by the JDOM Project (http://www.jdom.org/) This product includes software developed by The Apache Software Foundation (http://www.apache.org/) The license for JDOM can be read in the LICENSE.txt file in the source distribution available at http://www.jdom.org/ The license for the Commons Math library can be read at http://www.apache.org/licenses/LICENSE-2.0 or in the LICENSE.txt file in the source distribution available at http://jakarta.apache.org/commons/math/ This manual page and its XML source can be used, modified, and redistributed as if it were in public domain. &dhucpackage; &dhsection; &dhpackage; Bayesian Evolutionary Analysis Utility &dhpackage; nexus_file template_file beast_file DESCRIPTION BEAUti is a graphical user-interface (GUI) application for generating beast-mcmc(1) XML files. BUGS The &dhproduct; bug tracking system can be found at . SEE ALSO beast-mcmc 1 . REFERENCES Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7:214. Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88. Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185-1192. Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307-1320. debian/rules0000755000000000000000000000653312064152056010256 0ustar #!/usr/bin/make -f # -*- makefile -*- # debian/rules file for beast-mcmc # Andreas Tille # GPL #export DH_VERBOSE=1 PACKAGE := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') JAVA_HOME := /usr/lib/jvm/default-java DEBJAR := /usr/share/java CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:$(JAVA_HOME)/lib/tools.jar:$(DEBJAR)/beagle.jar:$(DEBJAR)/mpj.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:$(DEBJAR)/options.jar:$(DEBJAR)/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar # to run the test suite JAVA := $(JAVA_HOME)/bin/java ANT_HOME := /usr/share/ant ANT_BIN := $(ANT_HOME)/bin/ant ANT_ARGS := -Dcompile.debug=true -Dcompile.optimize=true %: dh $@ --with javahelper override_dh_auto_clean: rm -f native/*\.o native/*\.so native/*\.so\.* for cleantex in \ Practical_BEAST \ BookSection \ Practical_BEAST \ Yule \ SerialSampleCoalescent \ BEAST14_Manual \ ; do \ find doc -not -name "*.tex" -a -not -name "*.bib" -and -name "$${cleantex}.*" -exec rm -f \{\} \; ; \ done ant clean CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) PDFLATEX:=pdflatex -interaction=batchmode override_dh_auto_build: # CLASSPATH=$(CLASS_PATH) ant build ant -buildfile build_tracer.xml all # native/compileNativeLinux.sh does not create dynamic libraries cd native ; $(MAKE) -f Makefile.linux JAVA_HOME=$(JAVA_HOME) # gcc $(CFLAGS) $(LDFLAGS) -Wall -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ NucleotideLikelihoodCore.c -o libNucleotideLikelihoodCore.o ; \ # gcc -shared -Wl,-soname,libNucleotideLikelihoodCore.so.0 -o libNucleotideLikelihoodCore.so.0 libNucleotideLikelihoodCore.o -lc ; \ # gcc $(CFLAGS) $(LDFLAGS) -Wall -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ AminoAcidLikelihoodCore.c -o libAminoAcidLikelihoodCore.o ; \ # gcc -shared -Wl,-soname,libAminoAcidLikelihoodCore.so.0 -o libAminoAcidLikelihoodCore.so libAminoAcidLikelihoodCore.o -lc # # Build extra LaTeX documentation # cd doc/BookSection; $(PDFLATEX) BookSection.tex; $(PDFLATEX) BookSection.tex cd doc/tutorial/Virus_Practical*; $(PDFLATEX) Practical_BEAST.tex; $(PDFLATEX) Practical_BEAST.tex cd doc; $(PDFLATEX) Yule.tex; $(PDFLATEX) Yule.tex cd doc; $(PDFLATEX) SerialSampleCoalescent.tex; $(PDFLATEX) SerialSampleCoalescent.tex cd doc; $(PDFLATEX) BEAST14_Manual.tex; $(PDFLATEX) BEAST14_Manual.tex # ##################################################################### ## Run test suite ## ## -------------- ## ## While this test suite runs quite a bit of time (about 30min) it ## ## is recommended to be run at least once per new version upload ## ##################################################################### # # $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml junit override_dh_compress: dh_compress --exclude=.pdf get-orig-source: . debian/get-orig-source debian/libnucleotidelikelihoodcore0.links0000644000000000000000000000012012063644077016051 0ustar usr/lib/libNucleotideLikelihoodCore.so.0 usr/lib/libNucleotideLikelihoodCore.so debian/beast-mcmc.xpm0000644000000000000000000001164111775530153011741 0ustar /* XPM */ static char *beast_[] = { /* columns rows colors chars-per-pixel */ "32 32 125 2", " c #339C9AEADA00", ". c #3AB7A0CCDE9E", "X c #1DD39A39E533", "o c #22BD9A93E25F", "O c #2D609C83E2F4", "+ c #32139EECE3EB", "@ c #28FBA44EEC0B", "# c #3610A21AE3B7", "$ c #3C85A34FE472", "% c #30DDA3ADE883", "& c #2AC5B17FF6E6", "* c #2571BBC6F952", "= c #2855BE49F9D6", "- c #3C6DB692F442", "; 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Drummond Copyright holder for &dhproduct;. Andrew Rambaut Copyright holder for &dhproduct;. Marc A. Suchard Copyright holder for &dhproduct;. &dhfirstname; &dhsurname; Prepared this manpage in DocBook XML for the Debian distribution.
&dhemail;
2002–2010 Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard (&dhproduct;) 2009–2010 &dhusername; (This manpage) The binaries and source code are made available and can be distributed subject to the following conditions: BEAST is Copyright (C) 2002-2006 Alexei Drummond and Andrew Rambaut BEAST is distributed under the terms of the GNU Lesser General Public License. See the notice in individual files and the file LICENSE for licensing details. BEAST includes software libraries from projects whose licensing terms require that the following notices be included when they are distributed in binary form and that the recipient be given a copy of their respective licenses. This product includes software developed by the JDOM Project (http://www.jdom.org/) This product includes software developed by The Apache Software Foundation (http://www.apache.org/) The license for JDOM can be read in the LICENSE.txt file in the source distribution available at http://www.jdom.org/ The license for the Commons Math library can be read at http://www.apache.org/licenses/LICENSE-2.0 or in the LICENSE.txt file in the source distribution available at http://jakarta.apache.org/commons/math/ This manual page and its XML source can be used, modified, and redistributed as if it were in public domain. &dhucpackage; &dhsection; &dhpackage; Bayesian evolutionary analysis sampling trees &dhpackage; input.xml &dhpackage; DESCRIPTION BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It is intended both as a method of reconstructing phylogenies and as a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suite of programs for analysing the results. There are three main areas of research for which the BEAUti/BEAST package is particularly applicable. These areas are species phylogenies for molecular dating, coalescent-based population genetics and measurably evolving populations (ancient DNA or time-stamped viral sequence data sets). OPTIONS verbose XML parsing messages fail on non conforming BEAST XML file provide a console window display an options dialog change working directory to input file's directory specify a random number generator seed maximum number of numerical errors before stopping the number of computational threads to use (default 1) use Java only, no native implementations use beagle library if available show information on available beagle resources set order of beagle resources print usage screen BUGS The &dhproduct; bug tracking system can be found at . SEE ALSO beauti 1 . REFERENCES Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7:214. Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88. Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185-1192. Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307-1320. debian/upstream0000644000000000000000000000057411754732215010766 0ustar Reference: Author: Alexei J Drummond and Andrew Rambaut Title: "BEAST: Bayesian evolutionary analysis by sampling trees" Journal: BMC Evol Biol Year: 2007 Volume: 8 Number: 7 Pages: 214 DOI: 10.1186/1471-2148-7-214 PMID: 17996036 URL: http://www.biomedcentral.com/1471-2148/7/214/abstract eprint: http://www.biomedcentral.com/content/pdf/1471-2148-7-214.pdf debian/copyright0000644000000000000000000000371512112223633011122 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: BEAST-MCMC Upstream-Contact: Alexei Drummond , Andrew Rambaut Original-Source: http://beast-mcmc.googlecode.com/svn/trunk/ Files: src/dr/math/matrixAlgebra/RobustSingularValueDecomposition.java Copyright: 1999 CERN - European Organization for Nuclear Research 1999 Marc A. Suchard License: Colt License Agreement Permission to use, copy, modify, distribute and sell this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation. CERN makes no representations about the suitability of this software for any purpose. It is provided "as is" without expressed or implied warranty. Files: * Copyright: 2002-2011 Alexei Drummond and Andrew Rambaut License: LGPL-3+ Files: debian/* Copyright: 2011-2012 Andreas Tille License: LGPL-3+ License: LGPL-3+ This program 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 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 Lesser General Public License along with this program. If not, see . . On a Debian GNU/Linux system, the GNU Lesser GPL license version 3 is included in the file ‘/usr/share/common-licenses/LGPL-3’, and the GNU GPL license version 3 is included in the file ‘/usr/share/common-licenses/GPL-3’. debian/beast-mcmc-examples.install0000644000000000000000000000006511527003351014403 0ustar examples/release/* usr/share/doc/beast-mcmc/examples debian/beast-mcmc.menu0000644000000000000000000000067711775530176012115 0ustar ?package(beast-mcmc):\ needs="x11"\ section="Applications/Science/Biology"\ title="BEAST"\ command="/usr/bin/beast-mcmc"\ hints="Bayesian evolutionary analysis sampling trees"\ icon="/usr/share/pixmaps/beast-mcmc.xpm" ?package(beast-mcmc):\ needs="x11"\ section="Applications/Science/Biology"\ title="BEAUti"\ command="/usr/bin/beauti"\ hints="Bayesian Evolutionary Analysis Utility"\ icon="/usr/share/pixmaps/beauti.xpm" debian/source/0000755000000000000000000000000012063636004010466 5ustar debian/source/format0000644000000000000000000000001411473514012011672 0ustar 3.0 (quilt) debian/get-orig-source0000755000000000000000000000465511763133242012143 0ustar #!/bin/sh # get source for beast-mcmc from SVN because there is no source tarball distribution set -e NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` ORIGNAME=beast if ! echo $@ | grep -q upstream-version ; then VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` else VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${ORIGNAME}_release.*?\1?"` if echo "$VERSION" | grep -q "upstream-version" ; then echo "Unable to parse version number" exit fi fi SVNTAG=`echo ${VERSION} | sed 's/\./_/g'` rm -f ../${ORIGNAME}_release_${SVNTAG} RELEASE=${ORIGNAME}_release_${SVNTAG} TARDIR=${NAME}-${VERSION} mkdir -p ../tarballs cd ../tarballs # svn export conserves time stamps of the files, checkout does not LC_ALL=C svn export http://${NAME}.googlecode.com/svn/tags/${RELEASE} ${TARDIR} >/dev/null 2>/dev/null # remove jars which are provided as binaries but are not directly needed to build FigTree for jar in \ JRI.jar \ beagle.jar \ colt.jar \ commons-math-*.jar \ figtreepanel.jar \ itext-1.4.5.jar \ jam.jar \ jdom.jar \ jebl.jar \ junit-4.4.jar \ libjri.jnilib \ mpj.jar \ mtj.jar \ options.jar \ org.boehn.kmlframework_20090320.jar \ ; do rm -rf ${TARDIR}/lib/$jar done # No source available for phylogeography find ${TARDIR} -mindepth 1 -maxdepth 1 -name "*phylogeography*" | xargs rm -rf rm -rf ${TARDIR}/release/Mac ${TARDIR}/release/Windows ${TARDIR}/release/Linux/lib/* # Remove all preprocessed (duplicated!) docs rm -rf ${TARDIR}/release/common/doc/* # remove preprocessed docs which can be recreated using LaTeX to make sure that we # really have the source and to save some disk space in source archive for pdf in \ doc/SerialSampleCoalescent.pdf \ doc/Yule.pdf \ doc/tutorial/EBSP/ebsp-tut.pdf \ doc/tutorial/StarBEAST/STARBEAST.pdf \ ; do rm -rf ${TARDIR}/$pdf done # ... and every *.pdf named "Practical_" find ${TARDIR}/doc -name "Practical_*.pdf" -delete # There is no point in keeping LaTeX's *.aux files find ${TARDIR}/doc -name "*.aux" -delete GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.xz "${TARDIR}" rm -rf "${NAME}"-"$VERSION" debian/beast-mcmc.manpages0000644000000000000000000000001311523075104012706 0ustar debian/*.1 debian/beauti.10000644000000000000000000000624411400665731010532 0ustar .\" Title: BEAUTI .\" Author: Alexei J. Drummond .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: 05/28/2010 .\" Manual: BEAUti Manual .\" Source: BEAUti 1.5.3 .\" .TH "BEAUTI" "1" "05/28/2010" "BEAUti 1.5.3" "BEAUti Manual" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" beauti \- Bayesian Evolutionary Analysis Utility .SH "SYNOPSIS" .HP 7 \fBbeauti\fR [\fInexus_file\ template_file\ beast_file\fR] .SH "DESCRIPTION" .PP BEAUti is a graphical user\-interface (GUI) application for generating beast\-mcmc(1) XML files\&. .SH "BUGS" .PP The BEAUti bug tracking system can be found at \fI\%http://code.google.com/p/beast-mcmc/issues/list\fR\&. .SH "SEE ALSO" .PP \fBbeast-mcmc\fR(1)\&. .SH "REFERENCES" .sp .RS 4 \h'-04'\(bu\h'+03'Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees\&." BMC Evolutionary Biology 7:214\&. .RE .sp .RS 4 \h'-04'\(bu\h'+03'Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88\&. .RE .sp .RS 4 \h'-04'\(bu\h'+03'Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185\-1192\&. .RE .sp .RS 4 \h'-04'\(bu\h'+03'Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307\-1320\&. .RE .SH "AUTHORS" .PP \fBAlexei J\&. Drummond\fR .sp -1n .IP "" 4 Copyright holder for BEAUti\&. .PP \fBAndrew Rambaut\fR .sp -1n .IP "" 4 Copyright holder for BEAUti\&. .PP \fBMarc A\&. Suchard\fR .sp -1n .IP "" 4 Copyright holder for BEAUti\&. .PP \fBFelix Feyertag\fR <\&felix\&.feyertag@googlemail\&.com\&> .sp -1n .IP "" 4 Prepared this manpage in DocBook XML for the Debian distribution\&. .SH "COPYRIGHT" Copyright \(co 2002\(en2009 Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard (BEAUti) .br Copyright \(co 2002\(en2009 Felix Feyertag (This manpage) .br .PP The binaries and source code are made available and can be distributed subject to the following conditions: .PP BEAST is Copyright (C) 2002\-2006 Alexei Drummond and Andrew Rambaut BEAST is distributed under the terms of the GNU Lesser General Public License\&. See the notice in individual files and the file LICENSE for licensing details\&. .PP BEAST includes software libraries from projects whose licensing terms require that the following notices be included when they are distributed in binary form and that the recipient be given a copy of their respective licenses\&. .sp .RS 4 \h'-04'\(bu\h'+03'This product includes software developed by the JDOM Project (http://www\&.jdom\&.org/) .RE .sp .RS 4 \h'-04'\(bu\h'+03'This product includes software developed by The Apache Software Foundation (http://www\&.apache\&.org/) .RE .sp .RS 4 \h'-04'\(bu\h'+03'The license for JDOM can be read in the LICENSE\&.txt file in the source distribution available at http://www\&.jdom\&.org/ .RE .sp .RS 4 \h'-04'\(bu\h'+03'The license for the Commons Math library can be read at http://www\&.apache\&.org/licenses/LICENSE\-2\&.0 or in the LICENSE\&.txt file in the source distribution available at http://jakarta\&.apache\&.org/commons/math/ .RE .PP This manual page and its XML source can be used, modified, and redistributed as if it were in public domain\&. .sp debian/changelog0000644000000000000000000000341712151652074011050 0ustar beast-mcmc (1.7.5-1) unstable; urgency=low * New upstream version * Add debian/README.source explain why we stick to 1.7.x series for the moment -- Andreas Tille Thu, 30 May 2013 15:04:56 +0200 beast-mcmc (1.7.4-2) experimental; urgency=low * Add copyright license info for file (Closes: #698497). - src/dr/math/matrixAlgebra/RobustSingularValueDecomposition.java -- Olivier Sallou Sat, 23 Feb 2013 20:55:28 +0100 beast-mcmc (1.7.4-1) experimental; urgency=low * New upstream version (adapted patches) * debian/{control,rules}: use default java implementation thanks for the patch to James Page Closes: #683509 * debian/control: - rename beast-mcmc-lib to libnucleotidelikelihoodcore0 - Standards-Version: 3.9.4 (no changes needed) - do not depend from xterm any more - versioned (Build-)Depends from libhmsbeagle-java * Remove now unneeded lintian overrides * debian/patches/create_soname.patch: Create soname for library * debian/rules: silence pdflatex for better readable build logs -- Andreas Tille Mon, 17 Dec 2012 16:43:17 +0100 beast-mcmc (1.6.2-3) unstable; urgency=low * rename pixmap for menu to avoid name space conflict Closes: #680483 -- Andreas Tille Fri, 06 Jul 2012 11:30:19 +0200 beast-mcmc (1.6.2-2) unstable; urgency=low * debian/control: rename beast-doc to beast-mcmc-doc Closes: #679394 For consistency reasons also rename beast-examples to beast-mcmc-examples -- Andreas Tille Fri, 29 Jun 2012 11:24:51 +0200 beast-mcmc (1.6.2-1) unstable; urgency=low * Initial release. (Closes: #552101) -- Andreas Tille Tue, 05 Jun 2012 14:38:11 +0200 debian/patches/0000755000000000000000000000000012151647061010620 5ustar debian/patches/fix_classpath_in_build_tracer_xml.patch0000644000000000000000000001457012063636737020577 0ustar Author: Andreas Tille Date: Tue, 10 Jan 2012 22:29:24 +0100 Description: Make sure also tracer is builded with Debian packages JARs --- a/build_tracer.xml +++ b/build_tracer.xml @@ -32,6 +32,7 @@ + @@ -56,7 +57,7 @@ + classpath="${deblib}/colt.jar:${deblib}/commons-math.jar:${deblib}/jebl.jar:${deblib}/jam.jar:${deblib}/itext1.jar:${deblib}/jdom1.jar:${deblib}/mtj.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar:${deblib}/mpj.jar"> @@ -121,10 +122,10 @@ - - - - + + + + @@ -135,46 +136,12 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -199,55 +166,4 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - debian/patches/patch_tex_docs.patch0000644000000000000000000000315612063636703014640 0ustar Description: Fix some latex error that are preventing proper creation of docs Author: Andreas Tille Date: Tue, 05 Jun 2012 14:38:11 +0200 LastUpdated: Mon, 17 Dec 2012 16:43:17 +0100 --- a/doc/Yule.tex +++ b/doc/Yule.tex @@ -35,6 +35,7 @@ \begin{document} \title{\textbf{The Yule model}} +\date{22. May, 2007} \author{\textsc{Alexei J. Drummond}} --- a/doc/BookSection/BookSection.tex +++ b/doc/BookSection/BookSection.tex @@ -1,7 +1,7 @@ \NeedsTeXFormat{LaTeX2e}[1996/06/01] -\documentclass[cup7b, english]{cupbook} +\documentclass[english]{report} \usepackage{graphicx} @@ -32,6 +32,7 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands. \title{The Phylogenetics Handbook} +\date{September 14, 2007} \makeatother \begin{document} --- a/doc/SerialSampleCoalescent.tex +++ b/doc/SerialSampleCoalescent.tex @@ -33,7 +33,7 @@ \begin{document} \title{\textbf{The serially-sampled coalescent}} - +\date{July 12, 2007} \author{\textsc{Alexei J. Drummond}} \maketitle --- a/doc/BEAST14_Manual.tex +++ b/doc/BEAST14_Manual.tex @@ -35,7 +35,7 @@ \begin{document} \title{\textbf{A Rough Guide to BEAST 1.4}} - +\date{July 6, 2007} \author{\textsc{Alexei J. Drummond}$^{1}$, \textsc{Simon Y.W. Ho},\\ \textsc{Nic Rawlence} and \textsc{Andrew Rambaut}$^{2}$\\ --- a/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex +++ b/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex @@ -789,7 +789,7 @@ Define the prior not specified (marked a \medskip{} -\includegraphics[scale=0.4]{figures3/BEAUti_Prior} +\includegraphics[scale=0.4]{figures3/BEAUTi_Prior} \medskip{} debian/patches/create_soname.patch0000644000000000000000000000134512063643314014450 0ustar Description: Create SONAME for library Author: Andreas Tille Created: Mon, 17 Dec 2012 16:43:17 +0100 --- a/native/Makefile.linux +++ b/native/Makefile.linux @@ -1,11 +1,11 @@ CC=gcc -CFLAGS += -O2 -funroll-loops +CFLAGS=-O2 -funroll-loops INCLUDES=-I${JAVA_HOME}/include/ -I${JAVA_HOME}/include/linux OBJS = NucleotideLikelihoodCore.o .c.o: - ${CC} $(CPPFLAGS) ${CFLAGS} $(LDFLAGS) ${INCLUDES} -c $*.c + ${CC} ${CFLAGS} ${INCLUDES} -c $*.c libNucleotideLikelihoodCore.so: ${OBJS} - ${CC} $(CPPFLAGS) ${CFLAGS} $(LDFLAGS) ${INCLUDES} -shared -o libNucleotideLikelihoodCore.so ${OBJS} + ${CC} ${CFLAGS} ${INCLUDES} -shared -Wl,-soname,libNucleotideLikelihoodCore.so.0 -o libNucleotideLikelihoodCore.so ${OBJS} debian/patches/fix_classpath_in_build_xml.patch0000644000000000000000000001077412151647061017227 0ustar Author: Andreas Tille Last-Updated: 2012-02-26 Subject: use Debian jars Description: Make sure package builds with Debian packages JARs Forwarded: no --- a/build.xml +++ b/build.xml @@ -9,6 +9,7 @@ + @@ -21,6 +22,19 @@ + + + + + + + + + + + + + @@ -132,14 +146,6 @@ - - - - - - - - @@ -195,11 +201,6 @@ - - - - - --- a/.classpath +++ b/.classpath @@ -1,20 +1,20 @@ - - - - - - - - - + + + + + + + + + - - - + + + - + debian/patches/enable_hardening.patch0000644000000000000000000000130112151647055015104 0ustar Description: Enable propagation of hardening flags Author: Andreas Tille Date: Tue, 05 Jun 2012 14:38:11 +0200 --- a/native/Makefile.linux +++ b/native/Makefile.linux @@ -1,11 +1,11 @@ CC=gcc -CFLAGS=-O2 -funroll-loops +CFLAGS += -O2 -funroll-loops INCLUDES=-I${JAVA_HOME}/include/ -I${JAVA_HOME}/include/linux OBJS = NucleotideLikelihoodCore.o .c.o: - ${CC} ${CFLAGS} ${INCLUDES} -c $*.c + ${CC} $(CPPFLAGS) ${CFLAGS} $(LDFLAGS) ${INCLUDES} -c $*.c libNucleotideLikelihoodCore.so: ${OBJS} - ${CC} ${CFLAGS} ${INCLUDES} -shared -o libNucleotideLikelihoodCore.so ${OBJS} + ${CC} $(CPPFLAGS) ${CFLAGS} $(LDFLAGS) ${INCLUDES} -shared -o libNucleotideLikelihoodCore.so ${OBJS} debian/patches/series0000644000000000000000000000021112063643144012027 0ustar enable_hardening.patch fix_classpath_in_build_xml.patch patch_tex_docs.patch fix_classpath_in_build_tracer_xml.patch create_soname.patch debian/compat0000644000000000000000000000000211763415014010366 0ustar 9 debian/beast-mcmc-doc.install0000644000000000000000000000011611527001207013325 0ustar doc/*.pdf usr/share/doc/beast-mcmc doc/*/*.pdf usr/share/doc/beast-mcmc debian/beast-mcmc.manifest0000644000000000000000000000116211763416306012740 0ustar /usr/share/beast-mcmc/beast.jar: Main-Class: dr.app.beast.BeastMain Class-Path: /usr/share/java/beagle.jar /usr/share/java/commons-math.jar /usr/share/java/jdom1.jar /usr/share/java/jebl.jar /usr/share/java/jam.jar /usr/share/java/treeview.jar /usr/share/beast-mcmc/beauti.jar: Main-Class: dr.app.beauti.BeautiApp Class-Path: /usr/share/java/beagle.jar /usr/share/java/colt.jar /usr/share/java/commons-math.jar /usr/share/java/itext1-1.4.jar /usr/share/java/jam.jar /usr/share/java/jdom1.jar /usr/share/java/jebl.jar /usr/share/java/junit4.jar /usr/share/java/mpj.jar /usr/share/java/mtj.jar /usr/share/java/treeview.jar debian/beast-mcmc.install0000644000000000000000000000012711764176374012611 0ustar debian/bin usr debian/*.xpm usr/share/pixmaps build/dist/*.jar usr/share/beast-mcmc