.classpath

+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="lib" path="lib/beagle.jar"/>
+	<classpathentry kind="lib" path="lib/colt.jar"/>
+	<classpathentry kind="lib" path="lib/debug-1.0.jar"/>
+	<classpathentry kind="lib" path="lib/fest.jar"/>
+	<classpathentry kind="lib" path="lib/jam.jar"/>
+	<classpathentry kind="lib" path="lib/junit-4.8.2.jar"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="lib" path="lib/antlr-runtime-4.7.jar"/>
+	<classpathentry kind="lib" path="lib/commons-math3-3.6.1.jar" sourcepath="lib/commons-math3-3.6.1-sources.jar"/>
+	<classpathentry kind="output" path="build"/>
+</classpath>

debian/changelog

-beast2-mcmc (2.4.8+dfsg-1) UNRELEASED; urgency=medium
+beast2-mcmc (2.5.0+dfsg-1) unstable; urgency=medium
 
   [ Steffen Moeller ]
-  * d/control: Standards-Version: 4.1.3 (no changes required)
   * d/u/metadata:
     - added RRIDs
     - yamllint cleanliness 
@@ -14,8 +13,9 @@ beast2-mcmc (2.4.8+dfsg-1) UNRELEASED; urgency=medium
     Closes: #894359
   * Depends: s/openjdk-8-jre | java8-runtime/default-jre | java9-runtime/
   * d/rules: Add antlr4-runtime.jar to CLASS_PATH
+  * Standards-Version: 4.1.5
 
- -- Andreas Tille <tille@debian.org>  Fri, 06 Apr 2018 09:03:13 +0200
+ -- Andreas Tille <tille@debian.org>  Thu, 19 Jul 2018 08:20:21 +0200
 
 beast2-mcmc (2.4.4+dfsg-1) unstable; urgency=medium
 

debian/control

@@ -17,7 +17,7 @@ Build-Depends: debhelper (>= 11~),
                junit4,
                texlive-latex-base,
                texlive-latex-extra
-Standards-Version: 4.1.3
+Standards-Version: 4.1.4
 Vcs-Browser: https://salsa.debian.org/med-team/beast2-mcmc
 Vcs-Git: https://salsa.debian.org/med-team/beast2-mcmc.git
 Homepage: http://www.beast2.org

debian/patches/fix_classpath_in_build_xml.patch

@@ -38,12 +38,12 @@ Forwarded: no
      </path>
  
      <!--
-@@ -161,7 +161,7 @@
+@@ -174,7 +174,7 @@
          <mkdir dir="${release_dir}/package/lib" />
          <copy file="${dist}/beast.src.jar" todir="${release_dir}/package/"/>
          <copy file="${dist}/beast.jar" todir="${release_dir}/package/lib/"/>
 -        <copy file="../beast2/version.xml" todir="${release_dir}/package/"/>
 +        <copy file="version.xml" todir="${release_dir}/package/"/>
  
-         <jar jarfile="${release_dir}/package/BEAST.addon.v${version}.zip">
+         <jar jarfile="${release_dir}/package/BEAST.package.v${version}.zip">
              <fileset dir="${release_dir}/package">

debian/patches/remove_appbundler.patch

@@ -5,7 +5,7 @@ Description: Remove mac specific stuff breaking build on Linux when not
 
 --- a/build.xml
 +++ b/build.xml
-@@ -469,9 +469,6 @@
+@@ -689,9 +689,6 @@
          <echo message="cp BEAST.v${version}.tgz ~/tmp"/>
      </target>
  

examples/testOpSubSchedule.xml

+<beast version='2.0'
+       namespace='beast.evolution.alignment:beast.core:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood'>
+
+
+    <!-- The sequence alignment                                                  -->
+    <!-- ntax=6 nchar=768                                                        -->
+    <!-- npatterns=69                                                            -->
+    <data id="alignment" dataType="nucleotide">
+        <sequence taxon="human">
+            AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA
+        </sequence>
+        <sequence taxon="chimp">
+            AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA
+        </sequence>
+        <sequence taxon="bonobo">
+            AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA
+        </sequence>
+        <sequence taxon="gorilla">
+            AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA
+        </sequence>
+        <sequence taxon="orangutan">
+            AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA--CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA
+        </sequence>
+        <sequence taxon="siamang">
+            AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA
+        </sequence>
+    </data>
+
+    <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
+    <input spec='HKY' id='hky'>
+        <kappa idref='hky.kappa'/>
+        <frequencies id='freqs' spec='Frequencies'>
+            <data idref='alignment'/>
+        </frequencies>
+    </input>
+
+    <!-- site model                                                              -->
+    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
+        <!--
+            <parameter name='shape' id='shape' value='0.5'/>
+            <parameter name='proportionInvariant' id='propInvar' value='0.2'/>
+        -->
+        <substModel idref='hky'/>
+    </input>
+
+    <input spec='TreeLikelihood' id="treeLikelihood">
+        <data idref="alignment"/>
+        <tree idref="tree"/>
+        <siteModel idref="siteModel"/>
+    </input>
+
+    <parameter id="hky.kappa" value="1.0" lower="0.0"/>
+
+    <tree id='tree'/>
+
+    <tree spec='beast.util.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>
+        <taxa idref='alignment'/>
+    </tree>
+    <tree spec='beast.evolution.tree.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>
+        <populationModel spec='ConstantPopulation'>
+            <popSize spec='parameter.RealParameter' value='1'/>
+        </populationModel>
+    </tree>
+
+
+    <run spec="MCMC" id="mcmc" chainLength="1000000" preBurnin="50000">
+
+        <init idref='coalescentSimulator'/>
+        <distribution spec='CompoundDistribution' id='posterior'>
+            <distribution spec='beast.math.distributions.Prior' x='@hky.kappa'>
+                <distr spec='beast.math.distributions.OneOnX'/>
+            </distribution>
+            <distribution id='likelihood' idref="treeLikelihood"/>
+        </distribution>
+
+         <operatorschedule id="operatorSchedule" spec="OperatorSchedule">
+            <!-- assign 50% of total weight to operators that apply to the tree operations  -->
+            <subschedule id="operatorTrees" spec="OperatorSchedule" weight="50" weightIsPercentage="true" operatorPattern="^.*tree.*"/>
+         </operatorschedule>
+
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" parameter="@hky.kappa"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
+
+        <operator id='subtreeSlide' spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
+
+        <operator id='uniform' spec='Uniform' weight="10" tree="@tree"/>
+        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
+        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
+        <operator id='wilsonBalding' spec='WilsonBalding' weight="1" tree="@tree"/>
+
+        <logger logEvery="10000" fileName="test.$(seed).log">
+            <model idref='likelihood'/>
+            <log idref="likelihood"/>
+            <log idref='hky.kappa'/>
+            <log spec='beast.evolution.tree.TreeHeightLogger' tree='@tree'/>
+        </logger>
+        <logger logEvery="10000" fileName="test.$(seed).trees">
+            <log idref="tree"/>
+        </logger>
+        <logger logEvery="10000">
+            <model idref='likelihood'/>
+            <log idref="likelihood"/>
+            <ESS spec='ESS' name='log' arg="@likelihood"/>
+            <log idref='hky.kappa'/>
+            <ESS spec='ESS' name='log' arg="@hky.kappa"/>
+        </logger>
+    </run>
+
+</beast>

examples/testUCLNclock.json

-{version: "2.4",
+{version: "2.5",
 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.likelihood",
 
 beast: [

release/Linux/bin/applauncher

+#!/bin/sh
+
+if [ -z "$BEAST" ]; then
+	## resolve links - $0 may be a link to application
+	PRG="$0"
+
+	# need this for relative symlinks
+	while [ -h "$PRG" ] ; do
+	    ls=`ls -ld "$PRG"`
+	    link=`expr "$ls" : '.*-> \(.*\)$'`
+	    if expr "$link" : '/.*' > /dev/null; then
+		PRG="$link"
+	    else
+		PRG="`dirname "$PRG"`/$link"
+	    fi
+	done
+
+	# make it fully qualified
+	saveddir=`pwd`
+	BEAST0=`dirname "$PRG"`/..
+	BEAST=`cd "$BEAST0" && pwd`
+	cd "$saveddir"
+fi
+
+BEAST_LIB="$BEAST/lib"
+
+if [ -z "$JAVA_HOME" ]; then
+  JAVA=java
+else
+  JAVA=$JAVA_HOME/bin/java
+fi
+$JAVA -Dlauncher.wait.for.exit=true -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.tools.AppLauncherLauncher $*
+

release/Linux/bin/beast

@@ -52,7 +52,7 @@ 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 
-  $JAVA -Xms64m -Xmx4g -Djava.library.path=$BEAST_EXTRA_LIBS -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beastapp.BeastLauncher $*
+  $JAVA -Dlauncher.wait.for.exit=true -Xms64m -Xmx4g -Djava.library.path=$BEAST_EXTRA_LIBS -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beastapp.BeastLauncher $*
 else	
-  $JAVA -Xms64m -Xmx4g -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beastapp.BeastLauncher $*
+  $JAVA -Dlauncher.wait.for.exit=true -Xms64m -Xmx4g -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beastapp.BeastLauncher $*
 fi

release/Linux/bin/beauti

@@ -29,5 +29,5 @@ if [ -z "$JAVA_HOME" ]; then
 else
   JAVA=$JAVA_HOME/bin/java
 fi
-$JAVA -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beauti.BeautiLauncher -capture $*
+$JAVA -Dlauncher.wait.for.exit=true -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beauti.BeautiLauncher -capture $*
 

release/Linux/bin/logcombiner

@@ -29,5 +29,5 @@ if [ -z "$JAVA_HOME" ]; then
 else
   JAVA=$JAVA_HOME/bin/java
 fi
-$JAVA -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.tools.LogCombinerLauncher $*
+$JAVA -Dlauncher.wait.for.exit=true -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.tools.LogCombinerLauncher $*
 

release/Linux/bin/addonmanager → release/Linux/bin/packagemanager

@@ -29,5 +29,5 @@ if [ -z "$JAVA_HOME" ]; then
 else
   JAVA=$JAVA_HOME/bin/java
 fi
-$JAVA -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/beast.jar" beast.util.AddOnManager $*
+$JAVA -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/beast.jar" beast.util.PackageManager $*
 

release/Linux/bin/treeannotator

@@ -29,5 +29,5 @@ if [ -z "$JAVA_HOME" ]; then
 else
   JAVA=$JAVA_HOME/bin/java
 fi
-$JAVA -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.treeannotator.TreeAnnotatorLauncher $*
+$JAVA  -Dlauncher.wait.for.exit=true -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.treeannotator.TreeAnnotatorLauncher $*
 

release/Linux/jrebin/applauncher

+#!/bin/sh
+export JAVA_HOME=$(dirname "$0")/../jre1.8.0_161
+
+if [ -z "$BEAST" ]; then
+	## resolve links - $0 may be a link to application
+	PRG="$0"
+
+	# need this for relative symlinks
+	while [ -h "$PRG" ] ; do
+	    ls=`ls -ld "$PRG"`
+	    link=`expr "$ls" : '.*-> \(.*\)$'`
+	    if expr "$link" : '/.*' > /dev/null; then
+		PRG="$link"
+	    else
+		PRG="`dirname "$PRG"`/$link"
+	    fi
+	done
+
+	# make it fully qualified
+	saveddir=`pwd`
+	BEAST0=`dirname "$PRG"`/..
+	BEAST=`cd "$BEAST0" && pwd`
+	cd "$saveddir"
+fi
+
+BEAST_LIB="$BEAST/lib"
+
+if [ -z "$JAVA_HOME" ]; then
+  JAVA=java
+else
+  JAVA=$JAVA_HOME/bin/java
+fi
+$JAVA -Dlauncher.wait.for.exit=true -Dlauncher.wait.for.exit=true -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.tools.AppLauncherLauncher $*
+

release/Linux/jrebin/beast

+#!/bin/sh
+export JAVA_HOME=$(dirname "$0")/../jre1.8.0_161
+
+if [ -z "$BEAST" ]; then
+	## resolve links - $0 may be a link to application
+	PRG="$0"
+
+	# need this for relative symlinks
+	while [ -h "$PRG" ] ; do
+	    ls=`ls -ld "$PRG"`
+	    link=`expr "$ls" : '.*-> \(.*\)$'`
+	    if expr "$link" : '/.*' > /dev/null; then
+		PRG="$link"
+	    else
+		PRG="`dirname "$PRG"`/$link"
+	    fi
+	done
+
+	# make it fully qualified
+	saveddir=`pwd`
+	BEAST0=`dirname "$PRG"`/..
+	BEAST=`cd "$BEAST0" && pwd`
+	cd "$saveddir"
+fi
+
+BEAST_LIB="$BEAST/lib"
+
+if [ -z "$JAVA_HOME" ]; then
+  JAVA=java
+else
+  JAVA=$JAVA_HOME/bin/java
+fi
+
+
+# use BEAGLE_LIB if the BEAGLE library is not in a standard location
+if [ -n "$BEAGLE_LIB" ]; then
+	if [ -n "$BEAST_EXTRA_LIBS" ]; then
+		BEAST_EXTRA_LIBS=$BEAST_EXTRA_LIBS:$BEAGLE_LIB
+	else
+		BEAST_EXTRA_LIBS=$BEAGLE_LIB
+	fi
+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 [ -z "$LD_LIBRARY_PATH" ]; then
+    export LD_LIBRARY_PATH=/usr/local/lib
+else
+    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":/usr/local/lib
+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 
+  $JAVA -Dlauncher.wait.for.exit=true -Xms64m -Xmx4g -Djava.library.path=$BEAST_EXTRA_LIBS -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beastapp.BeastLauncher $*
+else	
+  $JAVA -Dlauncher.wait.for.exit=true -Xms64m -Xmx4g -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beastapp.BeastLauncher $*
+fi

release/Linux/jrebin/beauti

+#!/bin/sh
+export JAVA_HOME=$(dirname "$0")/../jre1.8.0_161
+
+if [ -z "$BEAST" ]; then
+	## resolve links - $0 may be a link to application
+	PRG="$0"
+
+	# need this for relative symlinks
+	while [ -h "$PRG" ] ; do
+	    ls=`ls -ld "$PRG"`
+	    link=`expr "$ls" : '.*-> \(.*\)$'`
+	    if expr "$link" : '/.*' > /dev/null; then
+		PRG="$link"
+	    else
+		PRG="`dirname "$PRG"`/$link"
+	    fi
+	done
+
+	# make it fully qualified
+	saveddir=`pwd`
+	BEAST0=`dirname "$PRG"`/..
+	BEAST=`cd "$BEAST0" && pwd`
+	cd "$saveddir"
+fi
+
+BEAST_LIB="$BEAST/lib"
+
+if [ -z "$JAVA_HOME" ]; then
+  JAVA=java
+else
+  JAVA=$JAVA_HOME/bin/java
+fi
+$JAVA -Dlauncher.wait.for.exit=true -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beauti.BeautiLauncher -capture $*
+

release/Linux/jrebin/densitree

+#!/bin/sh
+export JAVA_HOME=$(dirname "$0")/../jre1.8.0_161
+
+if [ -z "$BEAST" ]; then
+	## resolve links - $0 may be a link to application
+	PRG="$0"
+
+	# need this for relative symlinks
+	while [ -h "$PRG" ] ; do
+	    ls=`ls -ld "$PRG"`
+	    link=`expr "$ls" : '.*-> \(.*\)$'`
+	    if expr "$link" : '/.*' > /dev/null; then
+		PRG="$link"
+	    else
+		PRG="`dirname "$PRG"`/$link"
+	    fi
+	done
+
+	# make it fully qualified
+	saveddir=`pwd`
+	BEAST0=`dirname "$PRG"`/..
+	BEAST=`cd "$BEAST0" && pwd`
+	cd "$saveddir"
+fi
+
+BEAST_LIB="$BEAST/lib"
+
+if [ -z "$JAVA_HOME" ]; then
+  JAVA=java
+else
+  JAVA=$JAVA_HOME/bin/java
+fi
+$JAVA -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/DensiTree.jar:$BEAST/DensiTree.app/Contents/Java/DensiTree.jar" viz.DensiTree $*
+

release/Linux/jrebin/loganalyser

+#!/bin/sh
+export JAVA_HOME=$(dirname "$0")/../jre1.8.0_161
+
+if [ -z "$BEAST" ]; then
+	## resolve links - $0 may be a link to application
+	PRG="$0"
+
+	# need this for relative symlinks
+	while [ -h "$PRG" ] ; do
+	    ls=`ls -ld "$PRG"`
+	    link=`expr "$ls" : '.*-> \(.*\)$'`
+	    if expr "$link" : '/.*' > /dev/null; then
+		PRG="$link"
+	    else
+		PRG="`dirname "$PRG"`/$link"
+	    fi
+	done
+
+	# make it fully qualified
+	saveddir=`pwd`
+	BEAST0=`dirname "$PRG"`/..
+	BEAST=`cd "$BEAST0" && pwd`
+	cd "$saveddir"
+fi
+
+BEAST_LIB="$BEAST/lib"
+
+if [ -z "$JAVA_HOME" ]; then
+  JAVA=java
+else
+  JAVA=$JAVA_HOME/bin/java
+fi
+$JAVA -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/beast.jar" beast.util.LogAnalyser $*
+

release/Linux/jrebin/logcombiner

+#!/bin/sh
+export JAVA_HOME=$(dirname "$0")/../jre1.8.0_161
+
+if [ -z "$BEAST" ]; then
+	## resolve links - $0 may be a link to application
+	PRG="$0"
+
+	# need this for relative symlinks
+	while [ -h "$PRG" ] ; do
+	    ls=`ls -ld "$PRG"`
+	    link=`expr "$ls" : '.*-> \(.*\)$'`
+	    if expr "$link" : '/.*' > /dev/null; then
+		PRG="$link"
+	    else
+		PRG="`dirname "$PRG"`/$link"
+	    fi
+	done
+
+	# make it fully qualified
+	saveddir=`pwd`
+	BEAST0=`dirname "$PRG"`/..
+	BEAST=`cd "$BEAST0" && pwd`
+	cd "$saveddir"
+fi
+
+BEAST_LIB="$BEAST/lib"
+
+if [ -z "$JAVA_HOME" ]; then
+  JAVA=java
+else
+  JAVA=$JAVA_HOME/bin/java
+fi
+$JAVA -Dlauncher.wait.for.exit=true -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.tools.LogCombinerLauncher $*
+