New upstream version 1.10.2+dfsg (d0aeeeb4) · Commits · Debian Med / beast-mcmc

README.md

+1 −1

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		@@ -4,7 +4,7 @@ BEAST is a cross-platform program for Bayesian analysis of molecular sequences u

		## Download BEAST

		[Download BEAST v1.10.0 binaries for Mac, Windows and UNIX/Linux](https://github.com/beast-dev/beast-mcmc/releases/tag/v1.10.0)
		[Download BEAST v1.10.1 binaries for Mac, Windows and UNIX/Linux](https://github.com/beast-dev/beast-mcmc/releases/tag/v1.10.1)

		[The previous major release of BEAST was v1.8.4 --- binaries for Mac, Windows and UNIX/Linux](https://github.com/beast-dev/beast-mcmc/releases/tag/v1.8.4)

build.xml

+119 −13

Original line number	Diff line number	Diff line
		@@ -319,10 +319,10 @@
		<!--
		<property name="version" value="1.9"/>
		-->
		<property name="version" value="1.10.0"/>
		<property name="jvm_version" value="1.6+"/>
		<property name="version" value="1.10.2"/>
		<property name="jvm_version" value="1.7+"/>

		<property name="version_number" value="1.10.0"/>
		<property name="version_number" value="1.10.2"/>
		<property name="copyright" value="Copyright 2002-2018"/>

		<property name="release_dir" value="release"/>
		@@ -339,10 +339,12 @@
		<property name="Mac_dir" value="${release_dir}/Mac"/>
		<property name="Linux_dir" value="${release_dir}/Linux"/>
		<property name="Windows_dir" value="${release_dir}/Windows"/>
		<property name="Windows_launchers_dir" value="${release_dir}/Windows_Launchers"/>

		<property name="Mac_package_dir" value="${Mac_dir}/${BEAST_name} v${version}"/>
		<property name="Linux_package_dir" value="${Linux_dir}/${BEAST_name}v${version}"/>
		<property name="Windows_package_dir" value="${Windows_dir}/${BEAST_name} v${version}"/>
		<property name="Windows_launchers_package_dir" value="${Windows_launchers_dir}/${BEAST_name} v${version}"/>

		<!-- Need to either install Launch4j under {BEAST workspace}/${release}
		or install it in the default directory and change the location of launch4j.dir -->
		@@ -373,10 +375,11 @@
		</copy>
		<copy file="${dist}/beauti.jar" todir="${Windows_package_dir}/lib"/>
		<copy file="${dist}/beast.jar" todir="${Windows_package_dir}/lib"/>
		<!-- <copy file="${dist}/beast-beagle.jar" todir="${Windows_package_dir}/lib"/> -->
		<!--
		<copy todir="${Windows_package_dir}/lib">
		<fileset dir="${Windows_dir}/lib"/>
		</copy>
		-->
		<copy file="${common_dir}/VERSION HISTORY.txt" todir="${Windows_package_dir}"/>
		<copy file="${common_dir}/README.txt" todir="${Windows_package_dir}"/>

		@@ -398,6 +401,14 @@
		productVersion="${version_number}.0"
		txtProductVersion="${version}"/>

		<!-- BEAST v?.?.?.exe -->
		<launch4j configFile="${Windows_dir}/BEAST_launch4j.xml"
		outfile="${Windows_package_dir}/${BEAST_name} v${version}.exe"
		fileVersion="${version_number}.0"
		txtFileVersion="${version}"
		productVersion="${version_number}.0"
		txtProductVersion="${version}"/>

		<!-- TreeAnnotator v?.?.?.exe -->
		<launch4j configFile="${Windows_dir}/TreeAnnotator_launch4j.xml"
		jar="${dist}/beast.jar"
		@@ -440,6 +451,104 @@
		<echo message="Windows version release is finished."/>
		</target>

		<target name="windows_launchers" depends="dist"
		description="release Windows (launchers) version of BEAST, BEAUTI, TreeAnnotator, LogCombiner">

		<delete dir="${Windows_launchers_package_dir}"/>
		<!-- Create the release directory -->
		<mkdir dir="${Windows_launchers_package_dir}"/>

		<property name="launch4j.dir" location="${Windows_launchers_dir}/launch4j"/>
		<taskdef name="launch4j" classname="net.sf.launch4j.ant.Launch4jTask"
		classpath="${launch4j.dir}/launch4j.jar :${launch4j.dir}/lib/xstream.jar"/>

		<copy todir="${Windows_launchers_package_dir}/doc">
		<fileset dir="${common_dir}/doc"/>
		</copy>
		<copy todir="${Windows_launchers_package_dir}/examples">
		<fileset dir="examples"/>
		</copy>
		<copy todir="${Windows_launchers_package_dir}/native">
		<fileset dir="native">
		<exclude name="deprecated/**"/>
		</fileset>
		</copy>
		<copy todir="${Windows_launchers_package_dir}/bin">
		<fileset dir="${Windows_dir}/scripts"/>
		</copy>
		<copy file="${dist}/beauti.jar" todir="${Windows_launchers_package_dir}/lib"/>
		<copy file="${dist}/beast.jar" todir="${Windows_launchers_package_dir}/lib"/>
		<!--
		<copy todir="${Windows_package_dir}/lib">
		<fileset dir="${Windows_dir}/lib"/>
		</copy>
		-->
		<copy file="${common_dir}/VERSION HISTORY.txt" todir="${Windows_launchers_package_dir}"/>
		<copy file="${common_dir}/README.txt" todir="${Windows_launchers_package_dir}"/>

		<!-- BEAUTi v?.?.?.exe -->
		<launch4j configFile="${Windows_launchers_dir}/BEAUti_launch4j.xml"
		outfile="${Windows_launchers_package_dir}/${BEAUti_name} v${version}.exe"
		fileVersion="${version_number}.0"
		txtFileVersion="${version}"
		productVersion="${version_number}.0"
		txtProductVersion="${version}"/>

		<!-- BEAST v?.?.?.exe -->
		<launch4j configFile="${Windows_launchers_dir}/BEAST_launch4j.xml"
		outfile="${Windows_launchers_package_dir}/${BEAST_name} v${version}.exe"
		fileVersion="${version_number}.0"
		txtFileVersion="${version}"
		productVersion="${version_number}.0"
		txtProductVersion="${version}"/>

		<!-- BEAST v?.?.?.exe -->
		<launch4j configFile="${Windows_launchers_dir}/BEAST_launch4j.xml"
		outfile="${Windows_launchers_package_dir}/${BEAST_name} v${version}.exe"
		fileVersion="${version_number}.0"
		txtFileVersion="${version}"
		productVersion="${version_number}.0"
		txtProductVersion="${version}"/>

		<!-- TreeAnnotator v?.?.?.exe -->
		<launch4j configFile="${Windows_launchers_dir}/TreeAnnotator_launch4j.xml"
		outfile="${Windows_launchers_package_dir}/${TreeAnnotator_name} v${version}.exe"
		fileVersion="${version_number}.0"
		txtFileVersion="${version}"
		productVersion="${version_number}.0"
		txtProductVersion="${version}"/>

		<!-- LogCombiner v?.?.?.exe -->
		<launch4j configFile="${Windows_launchers_dir}/LogCombiner_launch4j.xml"
		outfile="${Windows_launchers_package_dir}/${LogCombiner_name} v${version}.exe"
		fileVersion="${version_number}.0"
		txtFileVersion="${version}"
		productVersion="${version_number}.0"
		txtProductVersion="${version}"/>

		<launch4j configFile="${Windows_launchers_dir}/TreeStat_launch4j.xml"
		outfile="${Windows_launchers_package_dir}/${TreeStat_name} v${version}.exe"
		fileVersion="${version_number}.0"
		txtFileVersion="${version}"
		productVersion="${version_number}.0"
		txtProductVersion="${version}"/>

		<!-- LogAnalyser v?.?.?.exe
		<launch4j configFile="${Windows_dir}/LogAnalyser_launch4j.xml"
		jar="${dist}/beast.jar"
		outfile="${Windows_package_dir}/${LogAnalyser_name}v${version}.exe"
		fileVersion="${version}.0"
		txtFileVersion="${version}"
		productVersion="${version}.0"
		txtProductVersion="${version}"/> -->

		<zip destfile="${release_dir}/${BEAST_name} v${version}_launchers.zip">
		<zipfileset dir="${Windows_launchers_package_dir}" prefix="${BEAST_name} v${version}"/>
		</zip>

		<echo message="Windows launchers version release is finished."/>
		</target>

		<target name="linux" depends="dist"
		description="release Linux/Unix version of BEAST, BEAUTI, TreeAnnotator, LogCombiner">
		<delete dir="${Linux_package_dir}"/>
		@@ -469,9 +578,6 @@
		<copy file="${dist}/beauti.jar" todir="${Linux_package_dir}/lib"/>
		<copy file="${dist}/beast.jar" todir="${Linux_package_dir}/lib"/>
		<!-- <copy file="${dist}/beast-beagle.jar" todir="${Linux_package_dir}/lib"/> -->
		<copy todir="${Linux_package_dir}/lib">
		<fileset dir="${Linux_dir}/lib"/>
		</copy>
		<copy file="${common_dir}/VERSION HISTORY.txt" todir="${Linux_package_dir}"/>
		<copy file="${common_dir}/README.txt" todir="${Linux_package_dir}"/>

		@@ -534,7 +640,7 @@
		useJavaXKey="true"
		icon="${common_dir}/icons/beast.icns"
		jvmversion="${jvm_version}"
		vmoptions="-d64 -Xmx2048M"
		vmoptions="-Xmx2048M"
		arguments="-window -working -options"
		highresolutioncapable="true"
		version="${version}"
		@@ -563,11 +669,11 @@
		<jarbundler dir="${Mac_package_dir}"
		name="${BEAUti_name} v${version}"
		mainclass="dr.app.beauti.BeautiApp"
		stubfile="${packaging_tools}/mac/universalJavaApplicationStub "
		stubfile="${packaging_tools}/mac/universalJavaApplicationStub_BEAST"
		useJavaXKey="true"
		icon="${common_dir}/icons/beauti.icns"
		jvmversion="${jvm_version}"
		vmoptions="-d64 -Xmx2048M"
		vmoptions="-Xmx2048M"
		arguments=""
		version="${version}"
		highresolutioncapable="true"
		@@ -606,7 +712,7 @@
		useJavaXKey="true"
		icon="${common_dir}/icons/utility.icns"
		jvmversion="${jvm_version}"
		vmoptions="-d64 -Xmx2048M"
		vmoptions="-Xmx2048M"
		highresolutioncapable="true"
		arguments=""
		version="${version}"
		@@ -635,7 +741,7 @@
		useJavaXKey="true"
		icon="${common_dir}/icons/utility.icns"
		jvmversion="${jvm_version}"
		vmoptions="-d64 -Xmx4096M"
		vmoptions="-Xmx4096M"
		highresolutioncapable="true"
		arguments=""
		version="${version}"
		@@ -664,7 +770,7 @@
		useJavaXKey="true"
		icon="${common_dir}/icons/TreeStat.icns"
		jvmversion="${jvm_version}"
		vmoptions="-d64 -Xmx1024M"
		vmoptions="-Xmx1024M"
		highresolutioncapable="true"
		arguments=""
		version="${version}"

build_tempest.xml

+3 −2

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		@@ -95,7 +95,7 @@
		</jar>
		</target>

		<property name="version" value="1.5.1" />
		<property name="version" value="1.5.2" />
		<property name="packaging_tools" value="packaging_tools" />
		<property name="release_dir" value="release_tempest" />
		<property name="name" value="TempEst" />
		@@ -198,7 +198,8 @@
		arguments=""
		vmoptions="-Xmx1024M"
		version="${version}"
		copyright="${name} v${version}, Copyright 2006-2017, Andrew Rambaut"
		highresolutioncapable="true"
		copyright="${name} v${version}, Copyright 2006-2018, Andrew Rambaut"
		bundleid="tempest" >
		<javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
		<jarfileset dir="${dist}">

examples/Benchmarks/benchmark1.xml

+18 −9

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		@@ -10114,7 +10114,7 @@
		<!-- throughout the time spanned by the genealogy. -->
		<constantSize id="constant" units="years">
		<populationSize>
		<parameter id="constant.popSize" value="52.0" lower="0.0" upper="Infinity"/>
		<parameter id="constant.popSize" value="52.0" lower="0.0"/>
		</populationSize>
		</constantSize>

		@@ -10153,7 +10153,7 @@
		<!-- The strict clock (Uniform rates across branches) -->
		<strictClockBranchRates id="branchRates">
		<rate>
		<parameter id="clock.rate" value="3.6E-4" lower="0.0" upper="Infinity"/>
		<parameter id="clock.rate" value="3.6E-4" lower="0.0"/>
		</rate>
		</strictClockBranchRates>

		@@ -10167,7 +10167,7 @@
		</frequencyModel>
		</frequencies>
		<kappa>
		<parameter id="kappa" value="2.0" lower="0.0" upper="Infinity"/>
		<parameter id="kappa" value="2.0" lower="0.0"/>
		</kappa>
		</HKYModel>

		@@ -10233,9 +10233,18 @@
		<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
		<parameter idref="kappa"/>
		</logNormalPrior>
		<oneOnXPrior>
		<dirichletPrior alpha="1.0" sumsTo="1.0">
		<parameter idref="frequencies"/>
		</dirichletPrior>
		<ctmcScalePrior>
		<ctmcScale>
		<parameter idref="clock.rate"/>
		</ctmcScale>
		<treeModel idref="treeModel"/>
		</ctmcScalePrior>
		<logNormalPrior mean="1.0" stdev="1.5" offset="0.0" meanInRealSpace="false">
		<parameter idref="constant.popSize"/>
		</oneOnXPrior>
		</logNormalPrior>
		<coalescentLikelihood idref="coalescent"/>
		</prior>
		<likelihood id="likelihood">
		@@ -10264,7 +10273,7 @@
		</log>

		<!-- write log to file -->
		<!--

		<log id="fileLog" logEvery="1000" fileName="benchmark1.log" overwrite="true">
		<posterior idref="posterior"/>
		<prior idref="prior"/>
		@@ -10283,7 +10292,7 @@
		<strictClockBranchRates idref="branchRates"/>
		<posterior idref="posterior"/>
		</logTree>
		-->

		</mcmc>
		<report>
		<property name="timer">

examples/Benchmarks/benchmark2.xml

+20 −8

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		@@ -647,7 +647,7 @@
		<!-- a Yule speciation process (a pure birth process). -->
		<yuleModel id="yule" units="substitutions">
		<birthRate>
		<parameter id="yule.birthRate" value="1.0" lower="0.0" upper="Infinity"/>
		<parameter id="yule.birthRate" value="1.0" lower="0.0"/>
		</birthRate>
		</yuleModel>

		@@ -708,19 +708,19 @@
		</frequencyModel>
		</frequencies>
		<rateAC>
		<parameter id="ac" value="1.0" lower="0.0" upper="Infinity"/>
		<parameter id="ac" value="1.0" lower="0.0"/>
		</rateAC>
		<rateAG>
		<parameter id="ag" value="1.0" lower="0.0" upper="Infinity"/>
		<parameter id="ag" value="1.0" lower="0.0"/>
		</rateAG>
		<rateAT>
		<parameter id="at" value="1.0" lower="0.0" upper="Infinity"/>
		<parameter id="at" value="1.0" lower="0.0"/>
		</rateAT>
		<rateCG>
		<parameter id="cg" value="1.0" lower="0.0" upper="Infinity"/>
		<parameter id="cg" value="1.0" lower="0.0"/>
		</rateCG>
		<rateGT>
		<parameter id="gt" value="1.0" lower="0.0" upper="Infinity"/>
		<parameter id="gt" value="1.0" lower="0.0"/>
		</rateGT>
		</gtrModel>

		@@ -730,7 +730,7 @@
		<gtrModel idref="gtr"/>
		</substitutionModel>
		<gammaShape gammaCategories="4">
		<parameter id="alpha" value="0.5" lower="0.0" upper="1000.0"/>
		<parameter id="alpha" value="0.5" lower="0.0"/>
		</gammaShape>
		</siteModel>
		<treeLikelihood id="treeLikelihood" useAmbiguities="false">
		@@ -812,6 +812,15 @@
		<gammaPrior shape="0.05" scale="10.0" offset="0.0">
		<parameter idref="gt"/>
		</gammaPrior>
		<exponentialPrior mean="0.5" offset="0.0">
		<parameter idref="alpha"/>
		</exponentialPrior>
		<dirichletPrior alpha="1.0" sumsTo="1.0">
		<parameter idref="frequencies"/>
		</dirichletPrior>
		<logNormalPrior mean="1.0" stdev="1.5" offset="0.0" meanInRealSpace="false">
		<parameter idref="yule.birthRate"/>
		</logNormalPrior>
		<speciationLikelihood idref="speciation"/>
		</prior>
		<likelihood id="likelihood">
		@@ -837,6 +846,9 @@
		<column label="clock.rate" sf="6" width="12">
		<parameter idref="clock.rate"/>
		</column>
		<column label="alpha" sf="6" width="12">
		<parameter idref="alpha"/>
		</column>
		</log>

		<!-- write log to file -->