[med-svn] [Git][med-team/beast2-mcmc][master] 6 commits: Update changelog
Andreas Tille (@tille)
gitlab at salsa.debian.org
Mon Oct 24 07:22:22 BST 2022
Andreas Tille pushed to branch master at Debian Med / beast2-mcmc
Commits:
3287404d by Andreas Tille at 2022-10-24T08:07:06+02:00
Update changelog
- - - - -
018ff60f by Andreas Tille at 2022-10-24T08:07:44+02:00
New upstream version 2.7.1+dfsg
- - - - -
e2c06f46 by Andreas Tille at 2022-10-24T08:07:44+02:00
routine-update: New upstream version
- - - - -
a5a6f156 by Andreas Tille at 2022-10-24T08:07:48+02:00
Update upstream source from tag 'upstream/2.7.1+dfsg'
Update to upstream version '2.7.1+dfsg'
with Debian dir bb834390254bcfc76644c471f162aedd06d72234
- - - - -
4ed4ae54 by Andreas Tille at 2022-10-24T08:07:53+02:00
Remove duplicate line from changelog.
Changes-By: lintian-brush
- - - - -
59046d2b by Andreas Tille at 2022-10-24T08:21:32+02:00
Mention new upstream version
- - - - -
25 changed files:
- build.xml
- debian/changelog
- − examples/nexus/dna.xml
- − examples/nexus/x.xml
- release/Linux/jrebin/applauncher
- release/Linux/jrebin/beast
- release/Linux/jrebin/loganalyser
- release/Windows/LogCombiner_launch4j_jre.xml
- release/Windows/bat/applauncher.bat
- release/Windows/bat/beast.bat
- release/Windows/bat/beauti.bat
- release/Windows/bat/loganalyser.bat
- release/Windows/bat/logcombiner.bat
- − release/Windows/bat/packagehealthchecker.bat
- release/Windows/bat/packagemanager.bat
- release/Windows/bat/treeannotator.bat
- release/common/README.txt
- release/common/VERSION HISTORY.txt
- scripts/migrate.pl
- src/beast/base/core/BEASTVersion2.java
- src/beast/pkgmgmt/BEASTClassLoader.java
- src/beast/pkgmgmt/BEASTVersion.java
- src/beast/pkgmgmt/launcher/BeastLauncher.java
- src/beast/pkgmgmt/launcher/TreeAnnotatorLauncher.java
- version.xml
Changes:
=====================================
build.xml
=====================================
@@ -97,6 +97,10 @@
includeAntRuntime='false'>
<include name="beast/pkgmgmt/**/**" />
</javac>
+
+ <copy todir="${build}">
+ <fileset dir="${beast2}/src" includes="**/*.png" />
+ </copy>
<jar jarfile="${build}/dist/launcher.jar">
<manifest>
=====================================
debian/changelog
=====================================
@@ -1,10 +1,16 @@
-beast2-mcmc (2.7.0+dfsg-1) UNRELEASED; urgency=medium
+beast2-mcmc (2.7.1+dfsg-1) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
+ * New upstream version
* Fix watch file
* New upstream version
* Standards-Version: 4.6.1 (routine-update)
+ * Adapt patches
+
+ [ Kieran Elmes ]
+ * include /usr/lib/x86_64-linux-gnu in java.library.path
- -- Andreas Tille <tille at debian.org> Tue, 20 Sep 2022 09:50:05 +0200
+ -- Andreas Tille <tille at debian.org> Mon, 24 Oct 2022 08:07:44 +0200
beast2-mcmc (2.6.7+dfsg-1) unstable; urgency=medium
=====================================
examples/nexus/dna.xml deleted
=====================================
@@ -1,121 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast beautitemplate='Standard' beautistatus='' namespace="beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihoodbeast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood" required="" version="2.7">
-
- <data
-id="dna"
-spec="beast.base.evolution.alignment.Alignment"
-name="alignment">
- <sequence id="seq_Carp" spec="beast.base.evolution.alignment.Sequence" taxon="Carp" totalcount="4" value="ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTTCTTCACTTCCACGACCACGCATTAATAATTGTGCTCCTAATTAGCACTTTAGTTTTATATATTATTACTGCAATGGTATCAACTAAACTTACTAATAAATATATTCTAGACTCCCAAGAAATCGAAATCGTATGAACCATTCTACCAGCCGTCATTTTAGTACTAATCGCCCTGCCCTCCCTACGCATCCTGTACCTTATAGACGAAATTAACGACCCTCACCTGACAATTAAAGCAATAGGACACCAATGATACTGAAGTTACGAGTATACAGACTATGAAAATCTAGGATTCGACTCCTATATAGTACCAACCCAAGACCTTGCCCCCGGACAATTCCGACTTCTGGAAACAGACCACCGAATAGTTGTTCCAATAGAATCCCCAGTCCGTGTCCTAGTATCTGCTGAAGACGTGCTACATTCTTGAGCTGTTCCATCCCTTGGCGTAAAAATGGACGCAGTCCCAGGACGACTAAATCAAGCCGCCTTTATTGCCTCACGCCCAGGGGTCTTTTACGGACAATGCTCTGAAATTTGTGGAGCTAATCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCTCTCGAACACTTCGAAAACTGATCCTCATTAATACTAGAAGACGCCTCGCTAGGAAGCTAA"/>
- <sequence id="seq_Chicken" spec="beast.base.evolution.alignment.Sequence" taxon="Chicken" totalcount="4" value="ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTCGTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTACCTTCTAACTCTTATACTTATAGAAAAACTATCA---TCAAACACCGTAGATGCCCAAGAAGTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTGCTTGCCCTCCCCTCCCTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATCGGACACCAATGATACTGAACCTATGAATACACAGACTTCAAGGACCTCTCATTTGACTCCTACATAACCCCAACAACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCATCGCATTGTAATCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTCCACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATCCCTGGACGACTAAATCAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGCGGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAAGCCTGATCCTCACTA------------------CTGTCATCTTAA"/>
- <sequence id="seq_Cow" spec="beast.base.evolution.alignment.Sequence" taxon="Cow" totalcount="4" value="ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTACTTCACTTTCATGACCACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTACATTATTTCACTAATACTAACGACAAAGCTGACCCATACAAGCACGATAGATGCACAAGAAGTAGAGACAATCTGAACCATTCTGCCCGCCATCATCTTAATTCTAATTGCTCTTCCTTCTTTACGAATTCTATACATAATAGATGAAATCAATAACCCATCTCTTACAGTAAAAACCATAGGACATCAGTGATACTGAAGCTATGAGTATACAGATTATGAGGACTTAAGCTTCGACTCCTACATAATTCCAACATCAGAATTAAAGCCAGGGGAGCTACGACTATTAGAAGTCGATAATCGAGTTGTACTACCAATAGAAATAACAATCCGAATGTTAGTCTCCTCTGAAGACGTATTACACTCATGAGCTGTGCCCTCTCTAGGACTAAAAACAGACGCAATCCCAGGCCGTCTAAACCAAACAACCCTTATATCGTCCCGTCCAGGCTTATATTACGGTCAATGCTCAGAAATTTGCGGGTCAAACCACAGTTTCATACCCATTGTCCTTGAGTTAGTCCCACTAAAGTACTTTGAAAAATGATCTGCGTCAATATTA---------------------TAA"/>
- <sequence id="seq_Frog" spec="beast.base.evolution.alignment.Sequence" taxon="Frog" totalcount="4" value="ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTACATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCTTATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAAAACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA"/>
- <sequence id="seq_Human" spec="beast.base.evolution.alignment.Sequence" taxon="Human" totalcount="4" value="ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATA---------------------GGGCCCGTATTTACCCTATAG"/>
- <sequence id="seq_Loach" spec="beast.base.evolution.alignment.Sequence" taxon="Loach" totalcount="4" value="ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTTCTTCACTTCCATGACCATGCCCTAATAATTGTATTTTTGATTAGCGCCCTAGTACTTTATGTTATTATTACAACCGTCTCAACAAAACTCACTAACATATATATTTTGGACTCACAAGAAATTGAAATCGTATGAACTGTGCTCCCTGCCCTAATCCTCATTTTAATCGCCCTCCCCTCACTACGAATTCTATATCTTATAGACGAGATTAATGACCCCCACCTAACAATTAAGGCCATGGGGCACCAATGATACTGAAGCTACGAGTATACTGATTATGAAAACTTAAGTTTTGACTCCTACATAATCCCCACCCAGGACCTAACCCCTGGACAATTCCGGCTACTAGAGACAGACCACCGAATGGTTGTTCCCATAGAATCCCCTATTCGCATTCTTGTTTCCGCCGAAGATGTACTACACTCCTGGGCCCTTCCAGCCATGGGGGTAAAGATAGACGCGGTCCCAGGACGCCTTAACCAAACCGCCTTTATTGCCTCCCGCCCCGGGGTATTCTATGGGCAATGCTCAGAAATCTGTGGAGCAAACCACAGCTTTATACCCATCGTAGTAGAAGCGGTCCCACTATCTCACTTCGAAAACTGGTCCACCCTTATACTAAAAGACGCCTCACTAGGAAGCTAA"/>
- <sequence id="seq_Mouse" spec="beast.base.evolution.alignment.Sequence" taxon="Mouse" totalcount="4" value="ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTAATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTATATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAAGTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCTCTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATAGGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCATATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAACCGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAATCAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGTGGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAAAACTGATCTGCTTCAATAATT---------------------TAA"/>
- <sequence id="seq_Rat" spec="beast.base.evolution.alignment.Sequence" taxon="Rat" totalcount="4" value="ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTTACAAACTTTCATGACCACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTATATTATTTCACTAATACTAACAACAAAACTAACACACACAAGCACAATAGACGCCCAAGAAGTAGAAACAATTTGAACAATTCTCCCAGCTGTCATTCTTATTCTAATTGCCCTTCCCTCCCTACGAATTCTATACATAATAGACGAGATTAATAACCCAGTTCTAACAGTAAAAACTATAGGACACCAATGATACTGAAGCTATGAATATACTGACTATGAAGACCTATGCTTTGACTCCTACATAATCCCAACCAATGACCTAAAACCAGGTGAACTTCGTCTATTAGAAGTTGATAATCGGGTAGTCTTACCAATAGAACTTCCAATTCGTATACTAATCTCATCCGAAGACGTCCTGCACTCATGAGCCATCCCTTCACTAGGGTTAAAAACCGACGCAATCCCCGGCCGCCTAAACCAAGCTACAGTCACATCAAACCGACCAGGTCTATTCTATGGCCAATGCTCTGAAATTTGCGGCTCAAATCACAGCTTCATACCCATTGTACTAGAAATAGTGCCTCTAAAATATTTCGAAAACTGATCAGCTTCTATAATT---------------------TAA"/>
- <sequence id="seq_Seal" spec="beast.base.evolution.alignment.Sequence" taxon="Seal" totalcount="4" value="ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTACTACACTTCCATGACCACACATTAATAATTGTGTTCCTAATTAGCTCATTAGTACTCTACATTATCTCACTTATACTAACCACGAAACTCACCCACACAAGTACAATAGACGCACAAGAAGTGGAAACGGTGTGAACGATCCTACCCGCTATCATTTTAATTCTCATTGCCCTACCATCATTACGAATCCTCTACATAATGGACGAGATCAATAACCCTTCCTTGACCGTAAAAACTATAGGACATCAGTGATACTGAAGCTATGAGTACACAGACTACGAAGACCTGAACTTTGACTCATATATGATCCCCACACAAGAACTAAAGCCCGGAGAACTACGACTGCTAGAAGTAGACAATCGAGTAGTCCTCCCAATAGAAATAACAATCCGCATACTAATCTCATCAGAAGATGTACTCCACTCATGAGCCGTACCGTCCCTAGGACTAAAAACTGATGCTATCCCAGGACGACTAAACCAAACAACCCTAATAACCATACGACCAGGACTGTACTACGGTCAATGCTCAGAAATCTGTGGTTCAAACCACAGCTTCATACCTATTGTCCTCGAATTGGTCCCACTATCCCACTTCGAGAAATGATCTACCTCAATGCTT---------------------TAA"/>
- <sequence id="seq_Whale" spec="beast.base.evolution.alignment.Sequence" taxon="Whale" totalcount="4" value="ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAAAAATGATCTGTATCAATACTA---------------------TAA"/>
- </data>
-
-
-
-
-<map name="Uniform" >beast.base.inference.distribution.Uniform</map>
-<map name="Exponential" >beast.base.inference.distribution.Exponential</map>
-<map name="LogNormal" >beast.base.inference.distribution.LogNormalDistributionModel</map>
-<map name="Normal" >beast.base.inference.distribution.Normal</map>
-<map name="Beta" >beast.base.inference.distribution.Beta</map>
-<map name="Gamma" >beast.base.inference.distribution.Gamma</map>
-<map name="LaplaceDistribution" >beast.base.inference.distribution.LaplaceDistribution</map>
-<map name="prior" >beast.base.inference.distribution.Prior</map>
-<map name="InverseGamma" >beast.base.inference.distribution.InverseGamma</map>
-<map name="OneOnX" >beast.base.inference.distribution.OneOnX</map>
-
-<run id="mcmc" spec="MCMC" chainLength="10000000">
- <state id="state" spec="State" storeEvery="5000">
- <tree id="Tree.t:dna" spec="beast.base.evolution.tree.Tree" name="stateNode">
- <taxonset id="TaxonSet.dna" spec="beast.base.evolution.alignment.TaxonSet">
- <alignment idref="dna"/>
- </taxonset>
- </tree>
- <parameter id="birthRate.t:dna" spec="parameter.RealParameter" name="stateNode">1.0</parameter>
- <parameter id="gammaShape.s:dna" spec="parameter.RealParameter" lower="0.1" name="stateNode">1.0</parameter>
- <parameter id="kappa.s:dna" spec="parameter.RealParameter" lower="0.0" name="stateNode">2.0</parameter>
- <parameter id="freqParameter.s:dna" spec="parameter.RealParameter" dimension="4" lower="0.0" name="stateNode" upper="1.0">0.25</parameter>
- </state>
- <init id="RandomTree.t:dna" spec="RandomTree" estimate="false" initial="@Tree.t:dna" taxa="@dna">
- <populationModel id="ConstantPopulation0.t:dna" spec="ConstantPopulation">
- <parameter id="randomPopSize.t:dna" spec="parameter.RealParameter" name="popSize">1.0</parameter>
- </populationModel>
- </init>
- <distribution id="posterior" spec="CompoundDistribution">
- <distribution id="prior" spec="CompoundDistribution">
- <distribution id="YuleModel.t:dna" spec="beast.base.evolution.speciation.YuleModel" birthDiffRate="@birthRate.t:dna" tree="@Tree.t:dna"/>
- <prior id="YuleBirthRatePrior.t:dna" name="distribution" x="@birthRate.t:dna">
- <Uniform id="Uniform.1" name="distr" upper="Infinity"/>
- </prior>
- <prior id="GammaShapePrior.s:dna" name="distribution" x="@gammaShape.s:dna">
- <Exponential id="Exponential.0" name="distr">
- <parameter id="RealParameter.0" spec="parameter.RealParameter" estimate="false" name="mean">1.0</parameter>
- </Exponential>
- </prior>
- <prior id="KappaPrior.s:dna" name="distribution" x="@kappa.s:dna">
- <LogNormal id="LogNormalDistributionModel.0" name="distr">
- <parameter id="RealParameter.1" spec="parameter.RealParameter" estimate="false" name="M">1.0</parameter>
- <parameter id="RealParameter.2" spec="parameter.RealParameter" estimate="false" name="S">1.25</parameter>
- </LogNormal>
- </prior>
- <prior id="FrequenciesPrior.s:dna" name="distribution" x="@freqParameter.s:dna">
- <Uniform id="Uniform.3" name="distr"/>
- </prior>
- </distribution>
- <distribution id="likelihood" spec="CompoundDistribution" useThreads="true">
- <distribution id="treeLikelihood.dna" spec="ThreadedTreeLikelihood" data="@dna" tree="@Tree.t:dna">
- <siteModel id="SiteModel.s:dna" spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape.s:dna">
- <parameter id="mutationRate.s:dna" spec="parameter.RealParameter" estimate="false" name="mutationRate">1.0</parameter>
- <parameter id="proportionInvariant.s:dna" spec="parameter.RealParameter" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
- <substModel id="hky.s:dna" spec="HKY" kappa="@kappa.s:dna">
- <frequencies id="estimatedFreqs.s:dna" spec="Frequencies" frequencies="@freqParameter.s:dna"/>
- </substModel>
- </siteModel>
- <branchRateModel id="StrictClock.c:dna" spec="beast.base.evolution.branchratemodel.StrictClockModel">
- <parameter id="clockRate.c:dna" spec="parameter.RealParameter" estimate="false" name="clock.rate">1.0</parameter>
- </branchRateModel>
- </distribution>
- </distribution>
- </distribution>
- <operator id="YuleBirthRateScaler.t:dna" spec="ScaleOperator" parameter="@birthRate.t:dna" weight="3.0"/>
- <operator id="YuleModelTreeScaler.t:dna" spec="ScaleOperator" scaleFactor="0.5" tree="@Tree.t:dna" weight="3.0"/>
- <operator id="YuleModelTreeRootScaler.t:dna" spec="ScaleOperator" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:dna" weight="3.0"/>
- <operator id="YuleModelUniformOperator.t:dna" spec="Uniform" tree="@Tree.t:dna" weight="30.0"/>
- <operator id="YuleModelSubtreeSlide.t:dna" spec="SubtreeSlide" tree="@Tree.t:dna" weight="15.0"/>
- <operator id="YuleModelNarrow.t:dna" spec="Exchange" tree="@Tree.t:dna" weight="15.0"/>
- <operator id="YuleModelWide.t:dna" spec="Exchange" isNarrow="false" tree="@Tree.t:dna" weight="3.0"/>
- <operator id="YuleModelWilsonBalding.t:dna" spec="WilsonBalding" tree="@Tree.t:dna" weight="3.0"/>
- <operator id="gammaShapeScaler.s:dna" spec="ScaleOperator" parameter="@gammaShape.s:dna" scaleFactor="0.5" weight="0.1"/>
- <operator id="KappaScaler.s:dna" spec="ScaleOperator" parameter="@kappa.s:dna" scaleFactor="0.5" weight="0.1"/>
- <operator id="FrequenciesExchanger.s:dna" spec="operator.DeltaExchangeOperator" delta="0.01" weight="0.1">
- <parameter idref="freqParameter.s:dna"/>
- </operator>
- <logger id="tracelog" spec="Logger" fileName="$(filebase).log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
- <log idref="posterior"/>
- <log idref="likelihood"/>
- <log idref="prior"/>
- <log idref="treeLikelihood.dna"/>
- <log id="TreeHeight.t:dna" spec="beast.base.evolution.tree.TreeHeightLogger" tree="@Tree.t:dna"/>
- <log idref="YuleModel.t:dna"/>
- <log idref="birthRate.t:dna"/>
- <log idref="gammaShape.s:dna"/>
- <log idref="kappa.s:dna"/>
- <log idref="freqParameter.s:dna"/>
- </logger>
- <logger id="screenlog" spec="Logger" logEvery="1000">
- <log idref="posterior"/>
- <log idref="likelihood"/>
- <log idref="prior"/>
- </logger>
- <logger id="treelog.t:dna" spec="Logger" fileName="$(tree).trees" logEvery="1000" mode="tree">
- <log id="TreeWithMetaDataLogger.t:dna" spec="beast.base.evolution.TreeWithMetaDataLogger" tree="@Tree.t:dna"/>
- </logger>
- <operatorschedule id="OperatorSchedule" spec="OperatorSchedule"/>
-</run>
-</beast>
=====================================
examples/nexus/x.xml deleted
=====================================
@@ -1,114 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast beautitemplate='Standard' beautistatus='' namespace="beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihoodbeast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood" required="" version="2.7">
-
- <data
-id="dna"
-spec="beast.base.evolution.alignment.Alignment"
-name="alignment">
- <sequence id="seq_Carp" spec="beast.base.evolution.alignment.Sequence" taxon="Carp" totalcount="4" value="ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTTCTTCACTTCCACGACCACGCATTAATAATTGTGCTCCTAATTAGCACTTTAGTTTTATATATTATTACTGCAATGGTATCAACTAAACTTACTAATAAATATATTCTAGACTCCCAAGAAATCGAAATCGTATGAACCATTCTACCAGCCGTCATTTTAGTACTAATCGCCCTGCCCTCCCTACGCATCCTGTACCTTATAGACGAAATTAACGACCCTCACCTGACAATTAAAGCAATAGGACACCAATGATACTGAAGTTACGAGTATACAGACTATGAAAATCTAGGATTCGACTCCTATATAGTACCAACCCAAGACCTTGCCCCCGGACAATTCCGACTTCTGGAAACAGACCACCGAATAGTTGTTCCAATAGAATCCCCAGTCCGTGTCCTAGTATCTGCTGAAGACGTGCTACATTCTTGAGCTGTTCCATCCCTTGGCGTAAAAATGGACGCAGTCCCAGGACGACTAAATCAAGCCGCCTTTATTGCCTCACGCCCAGGGGTCTTTTACGGACAATGCTCTGAAATTTGTGGAGCTAATCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCTCTCGAACACTTCGAAAACTGATCCTCATTAATACTAGAAGACGCCTCGCTAGGAAGCTAA"/>
- <sequence id="seq_Chicken" spec="beast.base.evolution.alignment.Sequence" taxon="Chicken" totalcount="4" value="ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTCGTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTACCTTCTAACTCTTATACTTATAGAAAAACTATCA---TCAAACACCGTAGATGCCCAAGAAGTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTGCTTGCCCTCCCCTCCCTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATCGGACACCAATGATACTGAACCTATGAATACACAGACTTCAAGGACCTCTCATTTGACTCCTACATAACCCCAACAACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCATCGCATTGTAATCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTCCACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATCCCTGGACGACTAAATCAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGCGGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAAGCCTGATCCTCACTA------------------CTGTCATCTTAA"/>
- <sequence id="seq_Cow" spec="beast.base.evolution.alignment.Sequence" taxon="Cow" totalcount="4" value="ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTACTTCACTTTCATGACCACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTACATTATTTCACTAATACTAACGACAAAGCTGACCCATACAAGCACGATAGATGCACAAGAAGTAGAGACAATCTGAACCATTCTGCCCGCCATCATCTTAATTCTAATTGCTCTTCCTTCTTTACGAATTCTATACATAATAGATGAAATCAATAACCCATCTCTTACAGTAAAAACCATAGGACATCAGTGATACTGAAGCTATGAGTATACAGATTATGAGGACTTAAGCTTCGACTCCTACATAATTCCAACATCAGAATTAAAGCCAGGGGAGCTACGACTATTAGAAGTCGATAATCGAGTTGTACTACCAATAGAAATAACAATCCGAATGTTAGTCTCCTCTGAAGACGTATTACACTCATGAGCTGTGCCCTCTCTAGGACTAAAAACAGACGCAATCCCAGGCCGTCTAAACCAAACAACCCTTATATCGTCCCGTCCAGGCTTATATTACGGTCAATGCTCAGAAATTTGCGGGTCAAACCACAGTTTCATACCCATTGTCCTTGAGTTAGTCCCACTAAAGTACTTTGAAAAATGATCTGCGTCAATATTA---------------------TAA"/>
- <sequence id="seq_Frog" spec="beast.base.evolution.alignment.Sequence" taxon="Frog" totalcount="4" value="ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTACATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCTTATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAAAACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA"/>
- <sequence id="seq_Human" spec="beast.base.evolution.alignment.Sequence" taxon="Human" totalcount="4" value="ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATA---------------------GGGCCCGTATTTACCCTATAG"/>
- <sequence id="seq_Loach" spec="beast.base.evolution.alignment.Sequence" taxon="Loach" totalcount="4" value="ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTTCTTCACTTCCATGACCATGCCCTAATAATTGTATTTTTGATTAGCGCCCTAGTACTTTATGTTATTATTACAACCGTCTCAACAAAACTCACTAACATATATATTTTGGACTCACAAGAAATTGAAATCGTATGAACTGTGCTCCCTGCCCTAATCCTCATTTTAATCGCCCTCCCCTCACTACGAATTCTATATCTTATAGACGAGATTAATGACCCCCACCTAACAATTAAGGCCATGGGGCACCAATGATACTGAAGCTACGAGTATACTGATTATGAAAACTTAAGTTTTGACTCCTACATAATCCCCACCCAGGACCTAACCCCTGGACAATTCCGGCTACTAGAGACAGACCACCGAATGGTTGTTCCCATAGAATCCCCTATTCGCATTCTTGTTTCCGCCGAAGATGTACTACACTCCTGGGCCCTTCCAGCCATGGGGGTAAAGATAGACGCGGTCCCAGGACGCCTTAACCAAACCGCCTTTATTGCCTCCCGCCCCGGGGTATTCTATGGGCAATGCTCAGAAATCTGTGGAGCAAACCACAGCTTTATACCCATCGTAGTAGAAGCGGTCCCACTATCTCACTTCGAAAACTGGTCCACCCTTATACTAAAAGACGCCTCACTAGGAAGCTAA"/>
- <sequence id="seq_Mouse" spec="beast.base.evolution.alignment.Sequence" taxon="Mouse" totalcount="4" value="ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTAATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTATATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAAGTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCTCTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATAGGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCATATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAACCGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAATCAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGTGGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAAAACTGATCTGCTTCAATAATT---------------------TAA"/>
- <sequence id="seq_Rat" spec="beast.base.evolution.alignment.Sequence" taxon="Rat" totalcount="4" value="ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTTACAAACTTTCATGACCACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTATATTATTTCACTAATACTAACAACAAAACTAACACACACAAGCACAATAGACGCCCAAGAAGTAGAAACAATTTGAACAATTCTCCCAGCTGTCATTCTTATTCTAATTGCCCTTCCCTCCCTACGAATTCTATACATAATAGACGAGATTAATAACCCAGTTCTAACAGTAAAAACTATAGGACACCAATGATACTGAAGCTATGAATATACTGACTATGAAGACCTATGCTTTGACTCCTACATAATCCCAACCAATGACCTAAAACCAGGTGAACTTCGTCTATTAGAAGTTGATAATCGGGTAGTCTTACCAATAGAACTTCCAATTCGTATACTAATCTCATCCGAAGACGTCCTGCACTCATGAGCCATCCCTTCACTAGGGTTAAAAACCGACGCAATCCCCGGCCGCCTAAACCAAGCTACAGTCACATCAAACCGACCAGGTCTATTCTATGGCCAATGCTCTGAAATTTGCGGCTCAAATCACAGCTTCATACCCATTGTACTAGAAATAGTGCCTCTAAAATATTTCGAAAACTGATCAGCTTCTATAATT---------------------TAA"/>
- <sequence id="seq_Seal" spec="beast.base.evolution.alignment.Sequence" taxon="Seal" totalcount="4" value="ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTACTACACTTCCATGACCACACATTAATAATTGTGTTCCTAATTAGCTCATTAGTACTCTACATTATCTCACTTATACTAACCACGAAACTCACCCACACAAGTACAATAGACGCACAAGAAGTGGAAACGGTGTGAACGATCCTACCCGCTATCATTTTAATTCTCATTGCCCTACCATCATTACGAATCCTCTACATAATGGACGAGATCAATAACCCTTCCTTGACCGTAAAAACTATAGGACATCAGTGATACTGAAGCTATGAGTACACAGACTACGAAGACCTGAACTTTGACTCATATATGATCCCCACACAAGAACTAAAGCCCGGAGAACTACGACTGCTAGAAGTAGACAATCGAGTAGTCCTCCCAATAGAAATAACAATCCGCATACTAATCTCATCAGAAGATGTACTCCACTCATGAGCCGTACCGTCCCTAGGACTAAAAACTGATGCTATCCCAGGACGACTAAACCAAACAACCCTAATAACCATACGACCAGGACTGTACTACGGTCAATGCTCAGAAATCTGTGGTTCAAACCACAGCTTCATACCTATTGTCCTCGAATTGGTCCCACTATCCCACTTCGAGAAATGATCTACCTCAATGCTT---------------------TAA"/>
- <sequence id="seq_Whale" spec="beast.base.evolution.alignment.Sequence" taxon="Whale" totalcount="4" value="ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAAAAATGATCTGTATCAATACTA---------------------TAA"/>
- </data>
-
-
-
-
-<map name="Uniform" >beast.base.inference.distribution.Uniform</map>
-<map name="Exponential" >beast.base.inference.distribution.Exponential</map>
-<map name="LogNormal" >beast.base.inference.distribution.LogNormalDistributionModel</map>
-<map name="Normal" >beast.base.inference.distribution.Normal</map>
-<map name="Beta" >beast.base.inference.distribution.Beta</map>
-<map name="Gamma" >beast.base.inference.distribution.Gamma</map>
-<map name="LaplaceDistribution" >beast.base.inference.distribution.LaplaceDistribution</map>
-<map name="prior" >beast.base.inference.distribution.Prior</map>
-<map name="InverseGamma" >beast.base.inference.distribution.InverseGamma</map>
-<map name="OneOnX" >beast.base.inference.distribution.OneOnX</map>
-
-<run id="mcmc" spec="MCMC" chainLength="10000000">
- <state id="state" spec="State" storeEvery="5000">
- <tree id="Tree.t:dna" spec="beast.base.evolution.tree.Tree" name="stateNode">
- <taxonset id="TaxonSet.dna" spec="beast.base.evolution.alignment.TaxonSet">
- <alignment idref="dna"/>
- </taxonset>
- </tree>
- <parameter id="birthRate.t:dna" spec="parameter.RealParameter" name="stateNode">1.0</parameter>
- <parameter id="kappa.s:dna" spec="parameter.RealParameter" lower="0.0" name="stateNode">2.0</parameter>
- <parameter id="freqParameter.s:dna" spec="parameter.RealParameter" dimension="4" lower="0.0" name="stateNode" upper="1.0">0.25</parameter>
- </state>
- <init id="RandomTree.t:dna" spec="RandomTree" estimate="false" initial="@Tree.t:dna" taxa="@dna">
- <populationModel id="ConstantPopulation0.t:dna" spec="ConstantPopulation">
- <parameter id="randomPopSize.t:dna" spec="parameter.RealParameter" name="popSize">1.0</parameter>
- </populationModel>
- </init>
- <distribution id="posterior" spec="CompoundDistribution">
- <distribution id="prior" spec="CompoundDistribution">
- <distribution id="YuleModel.t:dna" spec="beast.base.evolution.speciation.YuleModel" birthDiffRate="@birthRate.t:dna" tree="@Tree.t:dna"/>
- <prior id="YuleBirthRatePrior.t:dna" name="distribution" x="@birthRate.t:dna">
- <Uniform id="Uniform.1" name="distr" upper="Infinity"/>
- </prior>
- <prior id="KappaPrior.s:dna" name="distribution" x="@kappa.s:dna">
- <LogNormal id="LogNormalDistributionModel.0" name="distr">
- <parameter id="RealParameter.1" spec="parameter.RealParameter" estimate="false" name="M">1.0</parameter>
- <parameter id="RealParameter.2" spec="parameter.RealParameter" estimate="false" name="S">1.25</parameter>
- </LogNormal>
- </prior>
- <prior id="FrequenciesPrior.s:dna" name="distribution" x="@freqParameter.s:dna">
- <Uniform id="Uniform.3" name="distr"/>
- </prior>
- </distribution>
- <distribution id="likelihood" spec="CompoundDistribution" useThreads="true">
- <distribution id="treeLikelihood.dna" spec="ThreadedTreeLikelihood" data="@dna" tree="@Tree.t:dna">
- <siteModel id="SiteModel.s:dna" spec="SiteModel">
- <parameter id="mutationRate.s:dna" spec="parameter.RealParameter" estimate="false" name="mutationRate">1.0</parameter>
- <parameter id="gammaShape.s:dna" spec="parameter.RealParameter" estimate="false" name="shape">1.0</parameter>
- <parameter id="proportionInvariant.s:dna" spec="parameter.RealParameter" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
- <substModel id="hky.s:dna" spec="HKY" kappa="@kappa.s:dna">
- <frequencies id="estimatedFreqs.s:dna" spec="Frequencies" frequencies="@freqParameter.s:dna"/>
- </substModel>
- </siteModel>
- <branchRateModel id="StrictClock.c:dna" spec="beast.base.evolution.branchratemodel.StrictClockModel">
- <parameter id="clockRate.c:dna" spec="parameter.RealParameter" estimate="false" name="clock.rate">1.0</parameter>
- </branchRateModel>
- </distribution>
- </distribution>
- </distribution>
- <operator id="YuleBirthRateScaler.t:dna" spec="ScaleOperator" parameter="@birthRate.t:dna" weight="3.0"/>
- <operator id="YuleModelTreeScaler.t:dna" spec="ScaleOperator" scaleFactor="0.5" tree="@Tree.t:dna" weight="3.0"/>
- <operator id="YuleModelTreeRootScaler.t:dna" spec="ScaleOperator" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:dna" weight="3.0"/>
- <operator id="YuleModelUniformOperator.t:dna" spec="Uniform" tree="@Tree.t:dna" weight="30.0"/>
- <operator id="YuleModelSubtreeSlide.t:dna" spec="SubtreeSlide" tree="@Tree.t:dna" weight="15.0"/>
- <operator id="YuleModelNarrow.t:dna" spec="Exchange" tree="@Tree.t:dna" weight="15.0"/>
- <operator id="YuleModelWide.t:dna" spec="Exchange" isNarrow="false" tree="@Tree.t:dna" weight="3.0"/>
- <operator id="YuleModelWilsonBalding.t:dna" spec="WilsonBalding" tree="@Tree.t:dna" weight="3.0"/>
- <operator id="KappaScaler.s:dna" spec="ScaleOperator" parameter="@kappa.s:dna" scaleFactor="0.5" weight="0.1"/>
- <operator id="FrequenciesExchanger.s:dna" spec="operator.DeltaExchangeOperator" delta="0.01" weight="0.1">
- <parameter idref="freqParameter.s:dna"/>
- </operator>
- <logger id="tracelog" spec="Logger" fileName="$(filebase).log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
- <log idref="posterior"/>
- <log idref="likelihood"/>
- <log idref="prior"/>
- <log idref="treeLikelihood.dna"/>
- <log id="TreeHeight.t:dna" spec="beast.base.evolution.tree.TreeHeightLogger" tree="@Tree.t:dna"/>
- <log idref="YuleModel.t:dna"/>
- <log idref="birthRate.t:dna"/>
- <log idref="kappa.s:dna"/>
- <log idref="freqParameter.s:dna"/>
- </logger>
- <logger id="screenlog" spec="Logger" logEvery="10000">
- <log idref="posterior"/>
- <log idref="likelihood"/>
- <log idref="prior"/>
- </logger>
- <logger id="treelog.t:dna" spec="Logger" fileName="$(tree).trees" logEvery="1000" mode="tree">
- <log id="TreeWithMetaDataLogger.t:dna" spec="beast.base.evolution.TreeWithMetaDataLogger" tree="@Tree.t:dna"/>
- </logger>
- <operatorschedule id="OperatorSchedule" spec="OperatorSchedule"/>
-</run>
-</beast>
=====================================
release/Linux/jrebin/applauncher
=====================================
@@ -53,7 +53,7 @@ fi
# use BEAST_EXTRA_LIBS variable to load BEAGLE and other libraries from non-default locations
# this assumes that the library path contains all these libraries (or are set through LD_LIBRARY_PATH)
if [ -n "$BEAST_EXTRA_LIBS" ]; then
- "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path=$BEAST_EXTRA_LIBS -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher $*
+ "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher $*
else
"$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher $*
fi
=====================================
release/Linux/jrebin/beast
=====================================
@@ -31,9 +31,10 @@ else
JAVA="$JAVA_HOME"/bin/java
fi
+CPU=`uname -m`
# use BEAGLE_LIB if the BEAGLE library is not in a standard location
-if [[ $(uname -m) == 'x86_64' ]]; then
+if [ $CPU = 'x86_64' ]; then
if [ -n "$BEAGLE_LIB" ]; then
if [ -n "$BEAST_EXTRA_LIBS" ]; then
BEAST_EXTRA_LIBS="$BEAST_EXTRA_LIBS:$BEAGLE_LIB:$JAVA_HOME/lib/amd64"
@@ -46,7 +47,7 @@ fi
# Explicitly add /usr/local/lib to library search path to ensure
# beast continues to find beagle when installed here. (This is
# necessary due to known problems with certain JREs.)
-if [[ $(uname -m) == 'x86_64' ]]; then
+if [ $CPU = 'x86_64' ]; then
if [ -z "$LD_LIBRARY_PATH" ]; then
export LD_LIBRARY_PATH="/usr/local/lib:$JAVA_HOME/lib/amd64"
else
@@ -58,9 +59,9 @@ fi
# use BEAST_EXTRA_LIBS variable to load BEAGLE and other libraries from non-default locations
# this assumes that the library path contains all these libraries (or are set through LD_LIBRARY_PATH)
if [ -n "$BEAST_EXTRA_LIBS" ]; then
- if [[ $(uname -m) == 'x86_64' ]]; then
+ if [ $CPU = 'x86_64' ]; then
BEAST_EXTRA_LIBS="$JAVA_HOME/lib/amd64"
fi
fi
-"$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path=$LD_LIBRARY_PATH -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.BeastLauncher $*
+"$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path="$LD_LIBRARY_PATH" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.BeastLauncher $*
=====================================
release/Linux/jrebin/loganalyser
=====================================
@@ -53,7 +53,7 @@ fi
# use BEAST_EXTRA_LIBS variable to load BEAGLE and other libraries from non-default locations
# this assumes that the library path contains all these libraries (or are set through LD_LIBRARY_PATH)
if [ -n "$BEAST_EXTRA_LIBS" ]; then
- "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path=$BEAST_EXTRA_LIBS -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher LogAnalyser $*
+ "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher LogAnalyser $*
else
"$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher LogAnalyser $*
fi
=====================================
release/Windows/LogCombiner_launch4j_jre.xml
=====================================
@@ -2,15 +2,15 @@
<headerType>gui</headerType>
<icon>../common/icons/utility.ico</icon>
<classPath>
- <mainClass>bbeast.pkgmgmt.launcher.LogCombinerLauncher</mainClass>
+ <mainClass>beast.pkgmgmt.launcher.LogCombinerLauncher</mainClass>
<cp>./lib/launcher.jar</cp>
</classPath>
- <cmdLine></cmdLine>
<jre>
<minVersion>1.6.0</minVersion>
<initialHeapSize>256</initialHeapSize>
<maxHeapSize>8096</maxHeapSize>
<opt>-Duser.language=en</opt>
+ <path>jre</path>
</jre>
<versionInfo>
<fileDescription>LogCombiner</fileDescription>
=====================================
release/Windows/bat/applauncher.bat
=====================================
@@ -1,10 +1,12 @@
+ at echo off
+
REM Check whether the JRE is included
-IF EXIST %~dp0\..\jre (
+IF EXIST "%~dp0\..\jre" (
REM for BEAST version that includes JRE
- %~dp0\..\jre\bin\java -cp %~dp0\..\lib\launcher.jar beast.pkgmgmt.launcher.AppLauncherLauncher %*
+ "%~dp0\..\jre\bin\java" -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher %*
) ELSE (
REM for version that does not include JRE
- java -cp %~dp0\..\lib\launcher.jar beast.pkgmgmt.launcher.AppLauncherLauncher %*
+ java -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher %*
)
\ No newline at end of file
=====================================
release/Windows/bat/beast.bat
=====================================
@@ -1,10 +1,12 @@
+ at echo off
+
REM Check whether the JRE is included
IF EXIST %~dp0\..\jre (
REM for BEAST version that includes JRE
- %~dp0\..\jre\bin\java -cp %~dp0\..\lib\launcher.jar beast.pkgmgmt.launcher.BeastLauncher %*
+ "%~dp0\..\jre\bin\java" -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.launcher.BeastLauncher %*
) ELSE (
REM for version that does not include JRE
- java -cp %~dp0\..\lib\launcher.jar beast.pkgmgmt.launcher.BeastLauncher %*
+ java -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.launcher.BeastLauncher %*
)
\ No newline at end of file
=====================================
release/Windows/bat/beauti.bat
=====================================
@@ -1,10 +1,12 @@
+ at echo off
+
REM Check whether the JRE is included
-IF EXIST %~dp0\..\jre (
+IF EXIST "%~dp0\..\jre" (
REM for BEAST version that includes JRE
- %~dp0\..\jre\bin\java -cp %~dp0\..\lib\launcher.jar beast.pkgmgmt.launcher.BeautiLauncher %*
+ "%~dp0\..\jre\bin\java" -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.launcher.BeautiLauncher %*
) ELSE (
REM for version that does not include JRE
- java -cp %~dp0\..\lib\launcher.jar beast.pkgmgmt.launcher.BeautiLauncher %*
+ java -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.launcher.BeautiLauncher %*
)
\ No newline at end of file
=====================================
release/Windows/bat/loganalyser.bat
=====================================
@@ -1,10 +1,12 @@
+ at echo off
+
REM Check whether the JRE is included
-IF EXIST %~dp0\..\jre (
+IF EXIST "%~dp0\..\jre" (
REM for BEAST version that includes JRE
- %~dp0\..\jre\bin\java -cp %~dp0\..\lib\launcher.jar beast.pkgmgmt.launcher.AppLauncherLauncher LogAnalyser %*
+ "%~dp0\..\jre\bin\java" -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher LogAnalyser %*
) ELSE (
REM for version that does not include JRE
- java -cp %~dp0\..\lib\launcher.jar beast.pkgmgmt.launcher.AppLauncherLauncher LogAnalyser %*
+ java -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher LogAnalyser %*
)
\ No newline at end of file
=====================================
release/Windows/bat/logcombiner.bat
=====================================
@@ -1,10 +1,12 @@
+ at echo off
+
REM Check whether the JRE is included
-IF EXIST %~dp0\..\jre (
+IF EXIST "%~dp0\..\jre" (
REM for BEAST version that includes JRE
- %~dp0\..\jre\bin\java -cp %~dp0\..\lib\launcher.jar beast.pkgmgmt.launcher.LogCombinerLauncher %*
+ "%~dp0\..\jre\bin\java" -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.launcher.LogCombinerLauncher %*
) ELSE (
REM for version that does not include JRE
- java -cp %~dp0\..\lib\launcher.jar beast.pkgmgmt.launcher.LogCombinerLauncher %*
+ java -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.launcher.LogCombinerLauncher %*
)
\ No newline at end of file
=====================================
release/Windows/bat/packagehealthchecker.bat deleted
=====================================
@@ -1 +0,0 @@
-%~dp0\..\jre\bin\java -cp %~dp0\..\lib\launcher.jar beast.pkgmgmt.launcher.AppLauncherLauncher PackageHealthChecker %*
=====================================
release/Windows/bat/packagemanager.bat
=====================================
@@ -1,10 +1,12 @@
+ at echo off
+
REM Check whether the JRE is included
-IF EXIST %~dp0\..\jre (
+IF EXIST "%~dp0\..\jre" (
REM for BEAST version that includes JRE
- %~dp0\..\jre\bin\java -cp %~dp0\..\lib\launcher.jar beast.util.PackageManager %*
+ "%~dp0\..\jre\bin\java" -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.PackageManager %*
) ELSE (
REM for version that does not include JRE
- java -cp %~dp0\..\lib\launcher.jar beast.util.PackageManager %*
+ java -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.PackageManager %*
)
\ No newline at end of file
=====================================
release/Windows/bat/treeannotator.bat
=====================================
@@ -1,10 +1,12 @@
+ at echo off
+
REM Check whether the JRE is included
-IF EXIST %~dp0\..\jre (
+IF EXIST "%~dp0\..\jre" (
REM for BEAST version that includes JRE
- %~dp0\..\jre\bin\java -cp %~dp0\..\lib\launcher.jar beast.pkgmgmt.launcher.TreeAnnotatorLauncher %*
+ "%~dp0\..\jre\bin\java" -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.launcher.TreeAnnotatorLauncher %*
) ELSE (
REM for version that does not include JRE
- java -cp %~dp0\..\lib\launcher.jar beast.pkgmgmt.launcher.TreeAnnotatorLauncher %*
+ java -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.launcher.TreeAnnotatorLauncher %*
)
\ No newline at end of file
=====================================
release/common/README.txt
=====================================
@@ -1,7 +1,7 @@
- BEAST v2.7.0 2022
+ BEAST v2.7.1 2022
Beast 2 development team 2011-2022
-Last updated: September 2022
+Last updated: October 2022
Contents:
1) INTRODUCTION
@@ -129,6 +129,7 @@ BEAST arguments:
-DF as -D, but attribute-value pairs defined in file in JSON format
-DFout BEAST XML file written when -DF option is used
-sampleFromPrior samples from prior for MCMC analysis (by adding sampleFromPrior="true" in the first run element)
+ -version_file Provide a version file containing a list of services to explicitly allow. (Useful for package development.)
For example:
=====================================
release/common/VERSION HISTORY.txt
=====================================
@@ -1,10 +1,27 @@
- BEAST v2.7.0 2022
+ BEAST v2.7.1 2022
Beast 2 development team 2011-2022
Version History
-Last updated: August 2022
+Last updated: October 2022
All issues can be viewed at https://github.com/CompEvol/beast2/issues
================================================================================
+Version 2.7.1
+ Fix assorted launch issues on Windows, Mac and Linux
+ DocMaker functional again
+ Applauncher: deal with superfluous icon not found messages
+ EBSPanalyser converted to JavaFX
+ Logcombiner converted to JavaFX
+ BEAST: added option to specify version.xml files explicitly.
+ BEAUti:
+ o Fix some BEAUti tooltip glitches, and BEAUti icon in Windows
+ o Remove AquaFX theme.
+ o Fix splash screen for BEAUti
+ o Add theming to Alert
+ o More responsive refresh + do not loose list view selection
+ Clean up BEAST code and some BEAUti code
+ DensiTree update to v3.0.1, fixing a display bug on Apple Silicon
+ Update migration script for converting v2.6 packages to v2.7
+
Version 2.7.0
BEAUti has had a facelift, allows dark mode
BEAUti templates reorganised for better performance
=====================================
scripts/migrate.pl
=====================================
@@ -23,6 +23,7 @@ foreach $s (@s) {
$namespacemap{$1}=$2;
}
+
$s = 'beast.app.BEASTVersion beast.pkgmgmt.BEASTVersion
beast.app.BEASTVersion2 beast.base.core.BEASTVersion2
beast.app.BeastMCMC beastfx.app.beast.BeastMCMC
@@ -352,11 +353,27 @@ beast.math.distributions.WeibullDistribution beastlabs.math.distributions.Weibul
"BactrianSubtreeSlide" "beast.base.evolution.operator.kernel.BactrianSubtreeSlide"
"BactrianTipDatesRandomWalker" "beast.base.evolution.operator.kernel.BactrianTipDatesRandomWalker"
"BactrianUpDownOperator" "beast.base.inference.operator.kernel.BactrianUpDownOperator"
-';
+"LG" "beastclassic.evolution.substitutionmodel.LG"
+beast.inference.PathSampler modelselection.inference.PathSampler
+starbeast3.SpeciesTreePrior starbeast3.evolution.speciation.SpeciesTreePrior
+starbeast3.SpeciesTree starbeast3.tree.SpeciesTree
+starbeast3.GeneTreeForSpeciesTreeDistribution starbeast3.evolution.speciation.GeneTreeForSpeciesTreeDistribution
+starbeast3.StarBeast3Clock starbeast3.evolution.branchratemodel.StarBeast3Clock
+starbeast3.StarBeastStartState starbeast3.core.StarBeastStartState
+starbeast3.SpeciesTreeLogger starbeast3.core.SpeciesTreeLogger
+starbeast3.GeneTreeLogger beast.base.evolution.TreeWithMetaDataLogger
+beast.base.inference.OperatorScheduleRecalculator starbeast3.core.OperatorScheduleRecalculator
+beast.evolution.tree.RNNIMetric beastlabs.evolution.tree.RNNIMetric
+beast.base.evolution.tree.TreeDistanceLogger beastlabs.evolution.tree.TreeDistanceLogger
+"MultiGammaSiteModel" "mgsm.evolution.sitemodel.MultiGammaSiteModel"
+"MultiGammaSiteModelPrior" "mgsm.evolution.sitemodel.MultiGammaSiteModelPrior"
+"RelaxedGammaSiteModel" "mgsm.evolution.sitemodel.RelaxedGammaSiteModel"'
+;
if ($#ARGV < 0) {
- print "Usage: perl migrate.pl <directory>\n";
- print "Attempts to convert java class + xml files from BEAST v2.6.x to v2.7.0\n";
+ print "Usage: perl migrate.pl <directory or file>\n";
+ print "If a directory is specified, it recursively attempts to convert java class + xml files from BEAST v2.6.x to v2.7.0\n";
+ print "If a file is specified, only that file is converted.\n";
exit(0);
}
@s = split('\n',$s);
@@ -371,12 +388,19 @@ foreach $s (@s) {
$dir = $ARGV[0];
-open(FIN0,"find $dir|egrep \"java|xml\"|");
-while ($s = <FIN0>) {
- $s =~ s/\n//;
- process($s);
+if (-d $dir) {
+ open(FIN0,"find $dir|egrep \"java|xml\"|");
+ while ($s = <FIN0>) {
+ $s =~ s/\n//;
+ process($s);
+ }
+ close FIN0;
+} elsif (-e $dir) {
+ process($dir);
+} else {
+ print STDER "File or directory $dir could not be found.";
}
-close FIN0;
+
exit(0);
sub process {
@@ -396,6 +420,7 @@ sub process {
foreach $s (keys(%map)) {
$text =~ s/$s/$map{$s}/g;
}
+ $text =~ s/beast.base.evolution.tree.TreeWithMetaDataLogger/beast.base.evolution.TreeWithMetaDataLogger/g;
open(FOUT,">$file");
print FOUT $text;
close FOUT;
=====================================
src/beast/base/core/BEASTVersion2.java
=====================================
@@ -11,7 +11,7 @@ public class BEASTVersion2 extends BEASTVersion {
/**
* Version string: assumed to be in format x.x.x
*/
- private static final String VERSION = "2.7.0";
+ private static final String VERSION = "2.7.1";
private static final String DATE_STRING = "2002-2022";
=====================================
src/beast/pkgmgmt/BEASTClassLoader.java
=====================================
@@ -217,7 +217,7 @@ public class BEASTClassLoader extends URLClassLoader {
}
- private static void addServices(String versionFile) {
+ public static void addServices(String versionFile) {
try {
Map<String,Set<String>> services = null;
// print name and version of package
=====================================
src/beast/pkgmgmt/BEASTVersion.java
=====================================
@@ -17,7 +17,7 @@ public class BEASTVersion extends Version {
/**
* Version string: assumed to be in format x.x.x
*/
- private static final String VERSION = "2.7.0";
+ private static final String VERSION = "2.7.1";
private static final String DATE_STRING = "2002-2022";
=====================================
src/beast/pkgmgmt/launcher/BeastLauncher.java
=====================================
@@ -1,15 +1,10 @@
package beast.pkgmgmt.launcher;
+import beast.pkgmgmt.Package;
+import beast.pkgmgmt.*;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
-import beast.pkgmgmt.BEASTClassLoader;
-import beast.pkgmgmt.BEASTVersion;
-import beast.pkgmgmt.Package;
-import beast.pkgmgmt.PackageManager;
-import beast.pkgmgmt.PackageVersion;
-import beast.pkgmgmt.Utils6;
-
import javax.swing.*;
import javax.xml.parsers.DocumentBuilderFactory;
import java.io.*;
@@ -17,7 +12,10 @@ import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.net.URL;
import java.net.URLDecoder;
-import java.util.*;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
import java.util.jar.JarEntry;
import java.util.jar.JarInputStream;
@@ -568,12 +566,13 @@ public class BeastLauncher {
public static boolean testCudaStatusOnMac() {
- String beastJar = Utils6.getPackageUserDir();
- beastJar += "/" + "BEAST.base" + "/" + "lib" + "/" + "BEAST.base.jar";
- BeastLauncher clu = new BeastLauncher();
- String launcherJar = clu.getClass().getProtectionDomain().getCodeSource().getLocation().getPath();
- launcherJar = launcherJar.replaceAll("%20", "\\ ");
- return testCudaStatusOnMac(beastJar + File.pathSeparator + launcherJar, "beast.base.CudaDetector");
+ return true; // requested by Remco #1030
+// String beastJar = Utils6.getPackageUserDir();
+// beastJar += "/" + "BEAST.base" + "/" + "lib" + "/" + "BEAST.base.jar";
+// BeastLauncher clu = new BeastLauncher();
+// String launcherJar = clu.getClass().getProtectionDomain().getCodeSource().getLocation().getPath();
+// launcherJar = launcherJar.replaceAll("%20", "\\ ");
+// return testCudaStatusOnMac(beastJar + File.pathSeparator + launcherJar, "beast.base.CudaDetector");
}
/**
@@ -634,8 +633,9 @@ public class BeastLauncher {
return true;
}
}
- Process p = Runtime.getRuntime().exec(new String[]{java , "-Dbeast.user.package.dir=/NONE", "-cp" ,
- classPath , testCudaClass});
+ String [] args = new String[]{java , "-Dbeast.user.package.dir=/NONE", "-cp" ,
+ classPath.replaceAll(" ", "\\ "), testCudaClass};
+ Process p = Runtime.getRuntime().exec(args);
BufferedReader input = new BufferedReader(new InputStreamReader(p.getInputStream()));
int c;
while ((c = input.read()) != -1) {
=====================================
src/beast/pkgmgmt/launcher/TreeAnnotatorLauncher.java
=====================================
@@ -1,15 +1,10 @@
package beast.pkgmgmt.launcher;
-
import java.io.IOException;
import java.lang.reflect.InvocationTargetException;
-
-/**
- * Loads beast.jar and launches TreeAnnotator
- *
- * This class should be compiled against 1.6 and packaged by itself. The
- * remained of BEAST can be compiled against Java 1.7 or higher
+/** Launches TreeAnnotator
+ * @see BeastLauncher
* **/
public class TreeAnnotatorLauncher extends BeastLauncher {
=====================================
version.xml
=====================================
@@ -1,4 +1,4 @@
-<package name="BEAST.base" version="2.7.0">
+<package name="BEAST.base" version="2.7.1">
<!-- note version="2.7.x" must be double quotes for Mac release script release/Mac/createdmg.sh -->
<!-- data types -->
View it on GitLab: https://salsa.debian.org/med-team/beast2-mcmc/-/compare/5913ed2805d300dceaa7d9806706d220ac56206d...59046d2b6faf0be3263f5ffe4b68baf8eca803cd
--
View it on GitLab: https://salsa.debian.org/med-team/beast2-mcmc/-/compare/5913ed2805d300dceaa7d9806706d220ac56206d...59046d2b6faf0be3263f5ffe4b68baf8eca803cd
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20221024/b386cf6c/attachment-0001.htm>
More information about the debian-med-commit
mailing list