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BEASTGen packaging scripts
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‎build_beastgen.xml

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<project name="BEASTGen" default="build" basedir=".">
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<description>
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Build file for the phylogeography.jar tools package.
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$Id:$
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</description>
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<!-- set global properties for this build -->
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<property name="src" location="src"/>
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<property name="build" location="build"/>
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<property name="lib" location="lib"/>
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<property name="dist" location="dist"/>
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<path id="classpath">
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<fileset dir="${lib}" includes="**/*.jar"/>
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</path>
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<property environment="env"/>
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<target name="init">
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<!-- Create the time stamp -->
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<echo message="${ant.project.name}: ${ant.file}" />
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<tstamp/>
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<!-- Create the build directory structure used by compile -->
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<mkdir dir="${build}"/>
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<mkdir dir="${dist}"/>
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</target>
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<target name="compile" depends="init">
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<!-- Compile the java code from ${src} into ${build} -->
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<javac source="1.6" srcdir="${src}" destdir="${build}" classpathref="classpath">
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<include name="dr/app/beastgen/**"/>
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<include name="dr/app/beast/**"/>
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<include name="dr/app/util/**"/>
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<include name="dr/evolution/**"/>
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<include name="dr/inference/trace/**"/>
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<include name="dr/matrix/**"/>
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<include name="dr/stats/**"/>
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<include name="dr/math/**"/>
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<include name="dr/util/**"/>
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</javac>
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</target>
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<target name="build" depends="compile" description="generate the jar file">
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<!-- Create the distribution directory -->
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<mkdir dir="${dist}"/>
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<!-- Put everything in ${build} into the treestat.jar file -->
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<jar jarfile="${dist}/beastgen.jar">
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<manifest>
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<attribute name="Built-By" value="${user.name}"/>
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<attribute name="Main-Class" value="dr.app.beastgen.BEASTGen"/>
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</manifest>
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<fileset dir="${build}">
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<include name="dr/app/beastgen/**/*.class"/>
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<include name="dr/app/beast/BeastVersion.class"/>
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<include name="dr/app/util/**/*.class"/>
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<include name="dr/evolution/**/*.class"/>
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<include name="dr/inference/trace/**/*.class"/>
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<include name="dr/matrix/**/*.class"/>
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<include name="dr/stats/**/*.class"/>
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<include name="dr/math/**/*.class"/>
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<include name="dr/util/**/*.class"/>
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</fileset>
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<zipgroupfileset dir="${lib}" includes="**/freemarker.jar"/>
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<zipgroupfileset dir="${lib}" includes="**/jdom.jar"/>
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</jar>
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</target>
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<property name="version" value="1.0" />
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<property name="release_dir" value="release_beastgen" />
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<property name="name" value="BEASTGen" />
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<property name="common_dir" value="${release_dir}/common" />
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<property name="package_dir" value="${release_dir}/${name}_v${version}" />
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<target name="package" depends="build" description="release Linux/Unix version">
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<delete dir="${package_dir}" />
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<!-- Create the release directory -->
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<mkdir dir="${package_dir}" />
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<copy todir="${package_dir}/bin">
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<fileset dir="${common_dir}/bin"/>
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</copy>
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<copy todir="${package_dir}/templates">
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<fileset dir="${common_dir}/templates"/>
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</copy>
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<copy file="${dist}/beastgen.jar" todir="${package_dir}/lib"/>
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<copy file="${common_dir}/README.txt" todir="${package_dir}"/>
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<tar destfile="${release_dir}/${name}_v${version}.tgz" compression="gzip">
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<tarfileset dir="${package_dir}" prefix="${name}_v${version}"/>
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</tar>
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<zip destfile="${release_dir}/${name} v${version}.zip">
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<zipfileset dir="${package_dir}" prefix="${name} v${version}"/>
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</zip>
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<echo message="Linux/Unix version release is finished." />
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</target>
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</project>

‎release_beastgen/common/README.txt

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BEASTGen Tool
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This package contains a simple program for transforming data from one format to another.
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The program is run using the following command line:
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beastgen <template_filename> <input_filename> <output_filename>
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For example:
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beastgen to_fasta.template dengue.nex dengue.fasta
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This will change the NEXUS file into a FASTA file by using the to_fasta template (a FASTA
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to NEXUS template is also given in the templates folder).
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Also in the templates folder is 'beast_example.template' which demonstrates how to
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set up a template from a BEAST XML file.
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beastgen -chain_length 10000000 -log_every 1000 beast_example.template dengue.nex
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More detailed instructions are to be found on the BEAST website:
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http://beast.bio.ed.ac.uk/

‎release_phylogeography/common/bin/beastgen

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#!/bin/sh
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if [ -z "$BEASTGEN" ]; then
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## resolve links - $0 may be a link to application
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PRG="$0"
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# need this for relative symlinks
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while [ -h "$PRG" ] ; do
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ls=`ls -ld "$PRG"`
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link=`expr "$ls" : '.*-> \(.*\)$'`
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if expr "$link" : '/.*' > /dev/null; then
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PRG="$link"
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else
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PRG="`dirname "$PRG"`/$link"
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fi
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done
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# make it fully qualified
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saveddir=`pwd`
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BEASTGEN0=`dirname "$PRG"`/..
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BEASTGEN=`cd "$BEASTGEN0" && pwd`
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cd "$saveddir"
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fi
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BEASTGEN_LIB=$BEASTGEN/lib
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java -Xmx1024M -cp $BEASTGEN_LIB/beastgen.jar dr.app.beastgen.BEASTGen $*
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‎src/dr/app/beastgen/BEASTGen.java

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package beast;
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package dr.app.beastgen;
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import dr.app.util.Arguments;
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import dr.evolution.io.Importer;
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import freemarker.template.*;
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import java.io.*;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.StringTokenizer;
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public class BEASTGen {
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@@ -52,19 +50,6 @@ private Map constructDataModel(String inputFileName) throws IOException, Importe
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return root;
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}
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private int findArgument(String[] arguments, String label) {
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for (int i = 0; i < arguments.length; i++) {
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if (arguments[i].length() - 1 >= label.length()) {
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if (arguments[i].startsWith("-")) {
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}
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}
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}
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return -1;
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}
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public static String[] parseArguments(String[] arguments, Map dataModel) {
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int[] optionIndex = new int[arguments.length];

‎src/dr/app/beastgen/BeastImporter.java

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package beast;
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package dr.app.beastgen;
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import dr.evolution.alignment.Alignment;
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import dr.evolution.alignment.SimpleAlignment;

‎src/dr/app/beastgen/DataModelImporter.java

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package beast;
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package dr.app.beastgen;
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import dr.app.beauti.options.*;
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import dr.app.util.Utils;
@@ -322,7 +322,7 @@ private void setData(Map dataModel, String fileName, TaxonList taxonList, List<T
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checkTaxonList(taxonList);
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dataModel.put("taxa", createTaxonList(taxonList));
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dataModel.put("taxon_count", taxonList.getTaxonCount());
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dataModel.put("taxon_count", Integer.toString(taxonList.getTaxonCount()));
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if (taxonLists != null) {
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List<Map> tss = new ArrayList<Map>();
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}
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dataModel.put("alignment", createAlignment(alignment));
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dataModel.put("site_count", alignment.getSiteCount());
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dataModel.put("site_count", Integer.toString(alignment.getSiteCount()));
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dataModel.put("filename", fileName);
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dataModel.put("filename_stem", fileNameStem);

‎src/dr/app/beastgen/NexusApplicationImporter.java

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/*
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* NexusApplicationImporter.java
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*
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* Copyright (C) 2002-2011 Alexei Drummond and Andrew Rambaut
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*
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* This file is part of BEAST.
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* See the NOTICE file distributed with this work for additional
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* information regarding copyright ownership and licensing.
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*
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* BEAST is free software; you can redistribute it and/or modify
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* it under the terms of the GNU Lesser General Public License as
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* published by the Free Software Foundation; either version 2
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* of the License, or (at your option) any later version.
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*
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* BEAST is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public
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* License along with BEAST; if not, write to the
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* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
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* Boston, MA 02110-1301 USA
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*/
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package beast;
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package dr.app.beastgen;
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import dr.app.beauti.options.BeautiOptions;
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import dr.app.beauti.options.PartitionSubstitutionModel;

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