BEASTGen packaging scripts

beast-dev · Oct 17, 2013 · 3b05ed7 · 3b05ed7
1 parent 757045c
commit 3b05ed7
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Showing 10 changed files with 441 additions and 64 deletions.
diff --git a/build_beastgen.xml b/build_beastgen.xml
@@ -0,0 +1,103 @@
+<project name="BEASTGen" default="build" basedir=".">
+    <description>
+        Build file for the phylogeography.jar tools package.
+        $Id:$
+    </description>
+    <!-- set global properties for this build -->
+    <property name="src" location="src"/>
+    <property name="build" location="build"/>
+    <property name="lib" location="lib"/>
+    <property name="dist" location="dist"/>
+
+    <path id="classpath">
+		<fileset dir="${lib}" includes="**/*.jar"/>
+	</path>
+
+    <property environment="env"/>
+
+    <target name="init">
+        <!-- Create the time stamp -->
+        <echo message="${ant.project.name}: ${ant.file}" />
+        <tstamp/>
+        <!-- Create the build directory structure used by compile -->
+        <mkdir dir="${build}"/>
+        <mkdir dir="${dist}"/>
+    </target>
+
+    <target name="compile" depends="init">
+        <!-- Compile the java code from ${src} into ${build} -->
+        <javac source="1.6" srcdir="${src}" destdir="${build}" classpathref="classpath">
+            <include name="dr/app/beastgen/**"/>
+            <include name="dr/app/beast/**"/>
+            <include name="dr/app/util/**"/>
+            <include name="dr/evolution/**"/>
+            <include name="dr/inference/trace/**"/>
+            <include name="dr/matrix/**"/>
+            <include name="dr/stats/**"/>
+            <include name="dr/math/**"/>
+            <include name="dr/util/**"/>
+        </javac>
+    </target>
+
+    <target name="build" depends="compile" description="generate the jar file">
+        <!-- Create the distribution directory -->
+        <mkdir dir="${dist}"/>
+
+        <!-- Put everything in ${build} into the treestat.jar file -->
+        <jar jarfile="${dist}/beastgen.jar">
+            <manifest>
+                <attribute name="Built-By" value="${user.name}"/>
+                <attribute name="Main-Class" value="dr.app.beastgen.BEASTGen"/>
+            </manifest>
+            <fileset dir="${build}">
+                <include name="dr/app/beastgen/**/*.class"/>
+                <include name="dr/app/beast/BeastVersion.class"/>
+                <include name="dr/app/util/**/*.class"/>
+                <include name="dr/evolution/**/*.class"/>
+                <include name="dr/inference/trace/**/*.class"/>
+                <include name="dr/matrix/**/*.class"/>
+                <include name="dr/stats/**/*.class"/>
+                <include name="dr/math/**/*.class"/>
+                <include name="dr/util/**/*.class"/>
+            </fileset>
+            <zipgroupfileset dir="${lib}" includes="**/freemarker.jar"/>
+            <zipgroupfileset dir="${lib}" includes="**/jdom.jar"/>
+        </jar>
+    </target>
+
+    <property name="version" value="1.0" />
+    <property name="release_dir" value="release_beastgen" />
+    <property name="name" value="BEASTGen" />
+
+    <property name="common_dir" value="${release_dir}/common" />
+
+    <property name="package_dir" value="${release_dir}/${name}_v${version}" />
+
+    <target name="package" depends="build" description="release Linux/Unix version">
+        <delete dir="${package_dir}" />
+        <!-- Create the release directory -->
+        <mkdir dir="${package_dir}" />
+
+        <copy todir="${package_dir}/bin">
+            <fileset dir="${common_dir}/bin"/>
+        </copy>
+
+        <copy todir="${package_dir}/templates">
+            <fileset dir="${common_dir}/templates"/>
+        </copy>
+
+        <copy file="${dist}/beastgen.jar" todir="${package_dir}/lib"/>
+        <copy file="${common_dir}/README.txt" todir="${package_dir}"/>
+
+        <tar destfile="${release_dir}/${name}_v${version}.tgz" compression="gzip">
+            <tarfileset dir="${package_dir}" prefix="${name}_v${version}"/>
+        </tar>
+
+        <zip destfile="${release_dir}/${name} v${version}.zip">
+            <zipfileset dir="${package_dir}" prefix="${name} v${version}"/>
+        </zip>
+
+        <echo message="Linux/Unix version release is finished." />
+    </target>
+
+</project>
diff --git a/release_beastgen/common/README.txt b/release_beastgen/common/README.txt
@@ -0,0 +1,23 @@
+BEASTGen Tool
+
+This package contains a simple program for transforming data from one format to another.
+
+The program is run using the following command line:
+
+beastgen <template_filename> <input_filename> <output_filename>
+
+For example:
+
+beastgen to_fasta.template dengue.nex dengue.fasta
+
+This will change the NEXUS file into a FASTA file by using the to_fasta template (a FASTA
+to NEXUS template is also given in the templates folder).
+
+Also in the templates folder is 'beast_example.template' which demonstrates how to
+set up a template from a BEAST XML file.
+
+beastgen -chain_length 10000000 -log_every 1000 beast_example.template dengue.nex
+
+More detailed instructions are to be found on the BEAST website:
+
+http://beast.bio.ed.ac.uk/
diff --git a/release_phylogeography/common/bin/beastgen b/release_phylogeography/common/bin/beastgen
@@ -0,0 +1,27 @@
+#!/bin/sh
+
+if [ -z "$BEASTGEN" ]; 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"`/$link"
+	    fi
+	done
+
+	# make it fully qualified
+	saveddir=`pwd`
+	BEASTGEN0=`dirname "$PRG"`/..
+	BEASTGEN=`cd "$BEASTGEN0" && pwd`
+	cd "$saveddir"
+fi
+
+BEASTGEN_LIB=$BEASTGEN/lib
+java -Xmx1024M -cp $BEASTGEN_LIB/beastgen.jar dr.app.beastgen.BEASTGen $*
+
diff --git a/src/dr/app/beastgen/BEASTGen.java b/src/dr/app/beastgen/BEASTGen.java
@@ -1,13 +1,11 @@
-package beast;
+package dr.app.beastgen;
 
-import dr.app.util.Arguments;
 import dr.evolution.io.Importer;
 import freemarker.template.*;
 
 import java.io.*;
 import java.util.HashMap;
 import java.util.Map;
-import java.util.StringTokenizer;
 
 public class BEASTGen {
 
@@ -52,19 +50,6 @@ private Map constructDataModel(String inputFileName) throws IOException, Importe
         return root;
     }
 
-    private int findArgument(String[] arguments, String label) {
-        for (int i = 0; i < arguments.length; i++) {
-
-            if (arguments[i].length() - 1 >= label.length()) {
-                if (arguments[i].startsWith("-")) {
-
-                }
-            }
-        }
-        return -1;
-    }
-
-
     public static String[] parseArguments(String[] arguments, Map dataModel) {
 
         int[] optionIndex = new int[arguments.length];

diff --git a/src/dr/app/beastgen/BeastImporter.java b/src/dr/app/beastgen/BeastImporter.java
@@ -1,4 +1,4 @@
-package beast;
+package dr.app.beastgen;
 
 import dr.evolution.alignment.Alignment;
 import dr.evolution.alignment.SimpleAlignment;

diff --git a/src/dr/app/beastgen/DataModelImporter.java b/src/dr/app/beastgen/DataModelImporter.java
@@ -1,4 +1,4 @@
-package beast;
+package dr.app.beastgen;
 
 import dr.app.beauti.options.*;
 import dr.app.util.Utils;
@@ -322,7 +322,7 @@ private void setData(Map dataModel, String fileName, TaxonList taxonList, List<T
 
         checkTaxonList(taxonList);
         dataModel.put("taxa", createTaxonList(taxonList));
-        dataModel.put("taxon_count", taxonList.getTaxonCount());
+        dataModel.put("taxon_count", Integer.toString(taxonList.getTaxonCount()));
 
         if (taxonLists != null) {
             List<Map> tss = new ArrayList<Map>();
@@ -338,7 +338,7 @@ private void setData(Map dataModel, String fileName, TaxonList taxonList, List<T
         }
 
         dataModel.put("alignment", createAlignment(alignment));
-        dataModel.put("site_count", alignment.getSiteCount());
+        dataModel.put("site_count", Integer.toString(alignment.getSiteCount()));
 
         dataModel.put("filename", fileName);
         dataModel.put("filename_stem", fileNameStem);

diff --git a/src/dr/app/beastgen/NexusApplicationImporter.java b/src/dr/app/beastgen/NexusApplicationImporter.java
@@ -1,29 +1,4 @@
-/*
- * NexusApplicationImporter.java
- *
- * Copyright (C) 2002-2011 Alexei Drummond and Andrew Rambaut
- *
- * This file is part of BEAST.
- * See the NOTICE file distributed with this work for additional
- * information regarding copyright ownership and licensing.
- *
- * BEAST is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as
- * published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * BEAST is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with BEAST; if not, write to the
- * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
- * Boston, MA  02110-1301  USA
- */
-
-package beast;
+package dr.app.beastgen;
 
 import dr.app.beauti.options.BeautiOptions;
 import dr.app.beauti.options.PartitionSubstitutionModel;