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.gitignore
View file @ 93200f9e
......@@ -5,3 +5,4 @@ bin/
build/
dist/
out/
.idea
.idea/libraries/lib.xml deleted 100644 → 0
View file @ a00c73da
<component name="libraryTable">
<library name="lib">
<CLASSES>
<root url="file://$PROJECT_DIR$/lib" />
</CLASSES>
<JAVADOC />
<SOURCES />
<jarDirectory url="file://$PROJECT_DIR$/lib" recursive="false" />
</library>
</component>
\ No newline at end of file
.idea/uiDesigner.xml deleted 100644 → 0
View file @ a00c73da
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="Palette2">
<group name="Swing">
<item class="com.intellij.uiDesigner.HSpacer" tooltip-text="Horizontal Spacer" icon="/com/intellij/uiDesigner/icons/hspacer.png" removable="false" auto-create-binding="false" can-attach-label="false">
<default-constraints vsize-policy="1" hsize-policy="6" anchor="0" fill="1" />
</item>
<item class="com.intellij.uiDesigner.VSpacer" tooltip-text="Vertical Spacer" icon="/com/intellij/uiDesigner/icons/vspacer.png" removable="false" auto-create-binding="false" can-attach-label="false">
<default-constraints vsize-policy="6" hsize-policy="1" anchor="0" fill="2" />
</item>
<item class="javax.swing.JPanel" icon="/com/intellij/uiDesigner/icons/panel.png" removable="false" auto-create-binding="false" can-attach-label="false">
<default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3" />
</item>
<item class="javax.swing.JScrollPane" icon="/com/intellij/uiDesigner/icons/scrollPane.png" removable="false" auto-create-binding="false" can-attach-label="true">
<default-constraints vsize-policy="7" hsize-policy="7" anchor="0" fill="3" />
</item>
<item class="javax.swing.JButton" icon="/com/intellij/uiDesigner/icons/button.png" removable="false" auto-create-binding="true" can-attach-label="false">
<default-constraints vsize-policy="0" hsize-policy="3" anchor="0" fill="1" />
<initial-values>
<property name="text" value="Button" />
</initial-values>
</item>
<item class="javax.swing.JRadioButton" icon="/com/intellij/uiDesigner/icons/radioButton.png" removable="false" auto-create-binding="true" can-attach-label="false">
<default-constraints vsize-policy="0" hsize-policy="3" anchor="8" fill="0" />
<initial-values>
<property name="text" value="RadioButton" />
</initial-values>
</item>
<item class="javax.swing.JCheckBox" icon="/com/intellij/uiDesigner/icons/checkBox.png" removable="false" auto-create-binding="true" can-attach-label="false">
<default-constraints vsize-policy="0" hsize-policy="3" anchor="8" fill="0" />
<initial-values>
<property name="text" value="CheckBox" />
</initial-values>
</item>
<item class="javax.swing.JLabel" icon="/com/intellij/uiDesigner/icons/label.png" removable="false" auto-create-binding="false" can-attach-label="false">
<default-constraints vsize-policy="0" hsize-policy="0" anchor="8" fill="0" />
<initial-values>
<property name="text" value="Label" />
</initial-values>
</item>
<item class="javax.swing.JTextField" icon="/com/intellij/uiDesigner/icons/textField.png" removable="false" auto-create-binding="true" can-attach-label="true">
<default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
<preferred-size width="150" height="-1" />
</default-constraints>
</item>
<item class="javax.swing.JPasswordField" icon="/com/intellij/uiDesigner/icons/passwordField.png" removable="false" auto-create-binding="true" can-attach-label="true">
<default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
<preferred-size width="150" height="-1" />
</default-constraints>
</item>
<item class="javax.swing.JFormattedTextField" icon="/com/intellij/uiDesigner/icons/formattedTextField.png" removable="false" auto-create-binding="true" can-attach-label="true">
<default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
<preferred-size width="150" height="-1" />
</default-constraints>
</item>
<item class="javax.swing.JTextArea" icon="/com/intellij/uiDesigner/icons/textArea.png" removable="false" auto-create-binding="true" can-attach-label="true">
<default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
<preferred-size width="150" height="50" />
</default-constraints>
</item>
<item class="javax.swing.JTextPane" icon="/com/intellij/uiDesigner/icons/textPane.png" removable="false" auto-create-binding="true" can-attach-label="true">
<default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
<preferred-size width="150" height="50" />
</default-constraints>
</item>
<item class="javax.swing.JEditorPane" icon="/com/intellij/uiDesigner/icons/editorPane.png" removable="false" auto-create-binding="true" can-attach-label="true">
<default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
<preferred-size width="150" height="50" />
</default-constraints>
</item>
<item class="javax.swing.JComboBox" icon="/com/intellij/uiDesigner/icons/comboBox.png" removable="false" auto-create-binding="true" can-attach-label="true">
<default-constraints vsize-policy="0" hsize-policy="2" anchor="8" fill="1" />
</item>
<item class="javax.swing.JTable" icon="/com/intellij/uiDesigner/icons/table.png" removable="false" auto-create-binding="true" can-attach-label="false">
<default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
<preferred-size width="150" height="50" />
</default-constraints>
</item>
<item class="javax.swing.JList" icon="/com/intellij/uiDesigner/icons/list.png" removable="false" auto-create-binding="true" can-attach-label="false">
<default-constraints vsize-policy="6" hsize-policy="2" anchor="0" fill="3">
<preferred-size width="150" height="50" />
</default-constraints>
</item>
<item class="javax.swing.JTree" icon="/com/intellij/uiDesigner/icons/tree.png" removable="false" auto-create-binding="true" can-attach-label="false">
<default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
<preferred-size width="150" height="50" />
</default-constraints>
</item>
<item class="javax.swing.JTabbedPane" icon="/com/intellij/uiDesigner/icons/tabbedPane.png" removable="false" auto-create-binding="true" can-attach-label="false">
<default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3">
<preferred-size width="200" height="200" />
</default-constraints>
</item>
<item class="javax.swing.JSplitPane" icon="/com/intellij/uiDesigner/icons/splitPane.png" removable="false" auto-create-binding="false" can-attach-label="false">
<default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3">
<preferred-size width="200" height="200" />
</default-constraints>
</item>
<item class="javax.swing.JSpinner" icon="/com/intellij/uiDesigner/icons/spinner.png" removable="false" auto-create-binding="true" can-attach-label="true">
<default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1" />
</item>
<item class="javax.swing.JSlider" icon="/com/intellij/uiDesigner/icons/slider.png" removable="false" auto-create-binding="true" can-attach-label="false">
<default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1" />
</item>
<item class="javax.swing.JSeparator" icon="/com/intellij/uiDesigner/icons/separator.png" removable="false" auto-create-binding="false" can-attach-label="false">
<default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3" />
</item>
<item class="javax.swing.JProgressBar" icon="/com/intellij/uiDesigner/icons/progressbar.png" removable="false" auto-create-binding="true" can-attach-label="false">
<default-constraints vsize-policy="0" hsize-policy="6" anchor="0" fill="1" />
</item>
<item class="javax.swing.JToolBar" icon="/com/intellij/uiDesigner/icons/toolbar.png" removable="false" auto-create-binding="false" can-attach-label="false">
<default-constraints vsize-policy="0" hsize-policy="6" anchor="0" fill="1">
<preferred-size width="-1" height="20" />
</default-constraints>
</item>
<item class="javax.swing.JToolBar$Separator" icon="/com/intellij/uiDesigner/icons/toolbarSeparator.png" removable="false" auto-create-binding="false" can-attach-label="false">
<default-constraints vsize-policy="0" hsize-policy="0" anchor="0" fill="1" />
</item>
<item class="javax.swing.JScrollBar" icon="/com/intellij/uiDesigner/icons/scrollbar.png" removable="false" auto-create-binding="true" can-attach-label="false">
<default-constraints vsize-policy="6" hsize-policy="0" anchor="0" fill="2" />
</item>
</group>
</component>
</project>
\ No newline at end of file
.travis.yml
View file @ 93200f9e
language: java
sudo: false
jdk:
- oraclejdk7
- openjdk6
#jdk:
# - oraclejdk7
# - oraclejdk8
# - openjdk6
#addons:
# apt:
# packages:
# - ant-junit
script: ant dist
README.md
View file @ 93200f9e
# BEAST
Bayesian Evolutionary Analysis Sampling Trees (BEAST) is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
The program is orientated towards (strict and relaxed) molecular clock analyses.
It can be used as a method of constructing phylogenies, but it is also intended for testing evolutionary hypotheses without conditioning on a single tree topology.
BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.
It uses an XML input format that allows the user to design and run a large range of models.
We also include a program that can convert NEXUS files into this format.
BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
## Download BEAST
[Download BEAST v1.8.3 binaries for Mac, Windows and UNIX/Linux](http://tree.bio.ed.ac.uk/software/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)
[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)
[Older BEAST Downloads](https://code.google.com/p/beast-mcmc/downloads)
......@@ -21,14 +18,12 @@ We also include a program that can convert NEXUS files into this format.
# Documentation
[BEAST Documentation Website](http://beast.bio.ed.ac.uk)
[BEAST Documentation Website](http://beast.community)
# Acknowledgements
- This project is supported in part through the National Science Foundation grant DMS 1264153.
- This work was supported in part by the European Union Seventh Framework Programme for research, technological development and demonstration under Grant Agreement no. 278433-PREDEMICS and no. 725422-ReservoirDOCS, the Wellcome Trust through collaborator award 206298/Z/17/Z, NSF grant DMS 1264153 and NIH grants R01 HG006139, R01 AI107034 and U19 AI135995.
---
YourKit is kindly supporting open source projects with its full-featured Java Profiler.
YourKit, LLC is the creator of innovative and intelligent tools for profiling Java and .NET applications.
Take a look at YourKit's leading software products [YourKit Java Profiler](http://www.yourkit.com/java/profiler/index.jsp) and [YourKit .NET Profiler](http://www.yourkit.com/.net/profiler/index.jsp).
build.xml
View file @ 93200f9e
This diff is collapsed.
build_pathogen.xml deleted 100644 → 0
View file @ a00c73da
<project name="Pathogen" default="build" basedir=".">
<description>
Build file for PATHOGEN release versions, It is also used by Hudson Pathogen project.
$Id: build_pathogen.xml,v 1.5 2006/09/09 18:16:17 rambaut Exp $
</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="${dist}"/>
</target>
<target name="clean">
<delete dir="${build}"/>
</target>
<target name="compile" depends="init">
<!-- Compile the java code from ${src} into ${build} -->
<javac source="1.6" srcdir="${src}" destdir="${build}" classpathref="classpath">
<include name="dr/app/pathogen/**"/>
<include name="dr/app/beauti/**"/>
<include name="dr/app/tools/**"/>
<include name="dr/app/util/**"/>
<include name="dr/evolution/io/**"/>
<include name="dr/evolution/datatype/**"/>
<include name="dr/evolution/sequence/**"/>
<include name="dr/evolution/alignment/**"/>
<include name="dr/evolution/tree/**"/>
<include name="dr/evolution/util/**"/>
<include name="dr/app/gui/**"/>
<include name="dr/matrix/**"/>
<include name="dr/stats/**"/>
<include name="dr/math/**"/>
<include name="dr/util/**"/>
<include name="org/virion/jam/**"/>
</javac>
</target>
<target name="build" depends="compile" description="generate the jar file">
<!-- Create the distribution directory -->
<mkdir dir="${dist}"/>
<!-- Put everything in ${build} into the treestat.jar file -->
<jar jarfile="${dist}/pathogen.jar">
<manifest>
<attribute name="Built-By" value="${user.name}"/>
<attribute name="Main-Class" value="dr.app.pathogen.PathogenApp"/>
</manifest>
<fileset dir="${build}">
<include name="dr/app/pathogen/**/*.class"/>
<include name="dr/app/beauti/**/*.class"/>
<include name="dr/app/tools/**/*.class"/>
<include name="dr/app/util/**/*.class"/>
<include name="dr/evolution/io/**/*.class"/>
<include name="dr/evolution/datatype/**/*.class"/>
<include name="dr/evolution/sequence/**/*.class"/>
<include name="dr/evolution/alignment/**/*.class"/>
<include name="dr/evolution/tree/**/*.class"/>
<include name="dr/evolution/util/**/*.class"/>
<include name="dr/app/gui/**/*.class"/>
<include name="dr/matrix/**/*.class"/>
<include name="dr/stats/**/*.class"/>
<include name="dr/math/**/*.class"/>
<include name="dr/util/**/*.class"/>
</fileset>
<fileset dir="">
<include name="images/*.png"/>
</fileset>
<fileset dir="${src}">
<include name="dr/app/pathogen/**/*.png"/>
<include name="dr/app/gui/**/*.png"/>
<include name="org/virion/jam/**/*.png"/>
<include name="dr/gui/table/**/*.png"/>
</fileset>
<zipgroupfileset dir="${lib}" includes="**/jebl.jar"/>
<zipgroupfileset dir="${lib}" includes="**/jam.jar"/>
<zipgroupfileset dir="${lib}" includes="**/figtreepanel.jar"/>
</jar>
</target>
<property name="version" value="1.5" />
<property name="packaging_tools" value="packaging_tools" />
<property name="release_dir" value="release_pathogen" />
<property name="name" value="Path-O-Gen" />
<property name="common_dir" value="${release_dir}/common" />
<property name="Mac_dir" value="${release_dir}/Mac" />
<property name="Linux_dir" value="${release_dir}/Linux" />
<property name="Windows_dir" value="${release_dir}/Windows" />
<property name="Mac_package_dir" value="${Mac_dir}/${name} v${version}" />
<property name="Linux_package_dir" value="${Linux_dir}/${name}_v${version}" />
<property name="Windows_package_dir" value="${Windows_dir}/${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 -->
<target name="windows" depends="build" description="release Windows version of Pathogen">
<delete dir="${Windows_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Windows_package_dir}" />
<property name="launch4j.dir" location="${Windows_dir}/launch4j" />
<taskdef name="launch4j" classname="net.sf.launch4j.ant.Launch4jTask"
classpath="${launch4j.dir}/launch4j.jar :${launch4j.dir}/lib/xstream.jar" />
<copy file="${dist}/pathogen.jar" todir="${Windows_package_dir}/lib"/>
<copy todir="${Windows_package_dir}/lib">
<fileset dir="${Windows_dir}/lib"/>
</copy>
<copy file="${common_dir}/README.txt" todir="${Windows_package_dir}"/>
<launch4j configFile="${Windows_dir}/pathogen_launch4j.xml"
jar="${dist}/pathogen.jar"
outfile="${Windows_package_dir}/${name} v${version}.exe"
fileVersion="${version}.0.0"
txtFileVersion="${version}"
productVersion="${version}.0.0"
txtProductVersion="${version}"/>
<zip destfile="${release_dir}/${name} v${version}.zip">
<zipfileset dir="${Windows_package_dir}" prefix="${name} v${version}"/>
</zip>
<echo message="Windows version release is finished." />
</target>
<target name="linux" depends="build" description="release Linux/Unix version of Pathogen">
<delete dir="${Linux_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Linux_package_dir}" />
<copy todir="${Linux_package_dir}/bin">
<fileset dir="${Linux_dir}/scripts"/>
</copy>
<chmod dir="${Linux_package_dir}/bin" perm="755" includes="**/**"/>
<copy file="${Linux_dir}/icons/pathogen.png" todir="${Linux_package_dir}/images"/>
<copy file="${dist}/pathogen.jar" todir="${Linux_package_dir}/lib"/>
<copy todir="${Linux_package_dir}/lib">
<fileset dir="${Linux_dir}/lib"/>
</copy>
<copy file="${common_dir}/README.txt" todir="${Linux_package_dir}"/>
<tar destfile="${release_dir}/${name}_v${version}.tgz" compression="gzip">
<tarfileset dir="${Linux_package_dir}" prefix="${name}_v${version}"/>
</tar>
<echo message="Linux/Unix version release is finished." />
</target>
<target name="mac" depends="build" description="release Mac version of Pathogen">
<delete dir="${Mac_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Mac_package_dir}" />
<copy file="${common_dir}/README.txt" todir="${Mac_package_dir}"/>
<taskdef name="jarbundler" classname="net.sourceforge.jarbundler.JarBundler"/>
<!-- create a jar bundle for the mac -->
<jarbundler dir="${Mac_package_dir}"
name="${name} v${version}"
mainclass="dr.app.pathogen.PathogenApp"
stubfile="${packaging_tools}/mac/universalJavaApplicationStub"
icon="${Mac_dir}/icons/Path-O-Gen.icns"
jvmversion="1.6+"
arguments=""
version="${version}"
copyright="${name} v${version}, Copyright 2006-2015, Andrew Rambaut"
bundleid="pathogen" >
<javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
<jarfileset dir="${dist}">
<include name="**/pathogen.jar"/>
</jarfileset>
<jarfileset dir="${Mac_dir}/lib">
<include name="**/*.jar"/>
</jarfileset>
</jarbundler>
<echo message="Building disk image." />
<!-- create disk image -->
<exec executable="/usr/bin/hdiutil">
<arg value="create"/>
<arg value="-ov"/>
<arg value="-srcfolder"/>
<arg value="${Mac_package_dir}"/>
<arg value="-volname"/>
<arg value="${name} v${version}"/>
<arg value="-imagekey"/>
<arg value="zlib-level=6"/>
<arg value="${release_dir}/${name} v${version}.dmg"/>
</exec>
<echo message="Mac version release is finished." />
</target>
</project>
\ No newline at end of file
build_tempest.xml
View file @ 93200f9e
<!--
~ build_tempest.xml
~
~ Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
~
~ 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
-->
<project name="TempEst" default="build" basedir=".">
......@@ -54,7 +33,7 @@
<target name="compile" depends="init">
<!-- Compile the java code from ${src} into ${build} -->
<javac source="1.6" srcdir="${src}" destdir="${build}" classpathref="classpath">
<javac source="1.6" target="1.6" srcdir="${src}" destdir="${build}" classpathref="classpath">
<include name="dr/app/tempest/**"/>
<include name="dr/app/beauti/**"/>
<include name="dr/app/tools/**"/>
......@@ -74,7 +53,7 @@
</javac>
</target>
<target name="build" depends="compile" description="generate the jar file">
<target name="dist" depends="compile" description="generate the jar file">
<!-- Create the distribution directory -->
<mkdir dir="${dist}"/>
......@@ -116,7 +95,7 @@
</jar>
</target>
<property name="version" value="1.5" />
<property name="version" value="1.5.1" />
<property name="packaging_tools" value="packaging_tools" />
<property name="release_dir" value="release_tempest" />
<property name="name" value="TempEst" />
......@@ -133,7 +112,7 @@
<!-- Need to either install Launch4j under {BEAST workspace}/${release}
or install it in the default directory and change the location of launch4j.dir -->
<target name="windows" depends="build" description="release Windows version of TempEst">
<target name="windows" depends="dist" description="release Windows version of TempEst">
<delete dir="${Windows_package_dir}" />
<!-- Create the release directory -->
......@@ -156,9 +135,9 @@
<launch4j configFile="${Windows_dir}/tempest_launch4j.xml"
jar="${dist}/tempest.jar"
outfile="${Windows_package_dir}/${name} v${version}.exe"
fileVersion="${version}.0.0"
fileVersion="${version}.0"
txtFileVersion="${version}"
productVersion="${version}.0.0"
productVersion="${version}.0"
txtProductVersion="${version}"/>
<zip destfile="${release_dir}/${name} v${version}.zip">
......@@ -168,7 +147,7 @@
<echo message="Windows version release is finished." />
</target>
<target name="linux" depends="build" description="release Linux/Unix version of TempEst">
<target name="linux" depends="dist" description="release Linux/Unix version of TempEst">
<delete dir="${Linux_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Linux_package_dir}" />
......@@ -197,14 +176,17 @@
<echo message="Linux/Unix version release is finished." />
</target>
<target name="mac" depends="build" description="release Mac version of Tempest">
<!-- this will only work on Andrew's computer -->
<property name="AppleSigner" value="Developer ID Application: Andrew Rambaut (9E4WXAQ6SE)" />
<target name="mac" depends="dist" description="release Mac version of Tempest">
<delete dir="${Mac_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Mac_package_dir}" />
<copy file="${common_dir}/README.txt" todir="${Mac_package_dir}"/>
<taskdef name="jarbundler" classname="net.sourceforge.jarbundler.JarBundler"/>
<taskdef name="jarbundler" classname="com.ultramixer.jarbundler.JarBundler" classpath="${packaging_tools}/mac/jarbundler-core-3.3.0.jar"/>
<!-- create a jar bundle for the mac -->
<jarbundler dir="${Mac_package_dir}"
......@@ -216,7 +198,7 @@
arguments=""
vmoptions="-Xmx1024M"
version="${version}"
copyright="${name} v${version}, Copyright 2006-2016, Andrew Rambaut"
copyright="${name} v${version}, Copyright 2006-2017, Andrew Rambaut"
bundleid="tempest" >
<javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
<jarfileset dir="${dist}">
......@@ -224,6 +206,15 @@
</jarfileset>
</jarbundler>
<!-- code signing -->
<exec executable="codesign">
<arg value="--deep"/>
<arg value="-s"/>
<arg value="${AppleSigner}"/>
<arg value="-v"/>
<arg value="${Mac_package_dir}/${name} v${version}.app"/>
</exec>
<echo message="Building disk image." />
<!-- create disk image -->
......@@ -239,6 +230,16 @@
<arg value="${release_dir}/${name} v${version}.dmg"/>
</exec>
<exec executable="codesign">
<arg value="-s"/>
<arg value="${AppleSigner}"/>
<arg value="-v"/>
<arg value="${release_dir}/${name} v${version}.dmg"/>
</exec>
<echo message="Mac version release is finished." />
</target>
<target name="build" depends="mac, windows, linux" description="build all the executables" />
</project>
\ No newline at end of file
build_tracer.xml deleted 100644 → 0
View file @ a00c73da
<!--
~ build_tracer.xml
~
~ Copyright (C) 2002-2009 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
-->
<project name="Tracer_RELEASE" default="all" basedir=".">
<description>
Build file for BEAST release versions
$Id: build_release.xml,v 1.5 2006/09/09 18:16:17 rambaut Exp $
</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"/>
<property environment="env"/>
<target name="init">
<!-- Create the time stamp -->
<tstamp/>
<!-- Create the build directory structure used by compile -->
<mkdir dir="${build}"/>
<mkdir dir="${dist}"/>
</target>
<target name="all"
depends="compile-all"
description="Build all run-time stuff">
</target>
<target name="compile-all"
depends="compile-basic">
</target>
<target name="compile-basic" depends="init">
<!-- Compile the java code from ${src} into ${build} -->
<javac source="1.6" target="1.6" srcdir="${src}" destdir="${build}"
classpath="${lib}/colt.jar:${lib}/commons-math-2.2.jar:${lib}/jebl.jar:${lib}/jam.jar:${lib}/itext-1.4.5.jar:${lib}/jdom.jar:${lib}/mtj.jar:${lib}/JRI.jar:${lib}/mpj.jar">
<include name="dr/app/tracer/**"/>
<include name="dr/app/util/**"/>
<include name="dr/app/gui/**"/>
<include name="dr/app/java16compat/**/"/>
<include name="dr/evolution/alignment/**"/>
<include name="dr/evolution/coalescent/**"/>
<include name="dr/evolution/colouring/**"/>
<include name="dr/evolution/datatype/**"/>
<include name="dr/evolution/distance/**"/>
<include name="dr/evolution/io/**"/>
<include name="dr/evolution/parsimony/**"/>
<include name="dr/evolution/sequence/**"/>
<include name="dr/evolution/tree/**"/>
<include name="dr/evolution/util/**"/>
<include name="dr/inference/tracer/**"/>
<include name="dr/gui/chart/**"/>
<include name="dr/math/**"/>
<include name="dr/matrix/**"/>
<include name="dr/stats/**"/>
<include name="dr/util/**"/>
<include name="dr/xml/**"/>
</javac>
</target>
<target name="dist" depends="compile-all"
description="generate the distribution">
<!-- Create the distribution directory -->
<mkdir dir="${dist}"/>
<!-- Put everything in ${build} into the beast.jar file -->
<jar jarfile="${dist}/tracer.jar">
<manifest>
<attribute name="Built-By" value="${user.name}"/>
<attribute name="Main-Class" value="dr.app.tracer.application.TracerApp"/>
</manifest>
<fileset dir="${build}">
<include name="dr/app/tracer/**/*.class"/>
<include name="dr/app/gui/**/*.class"/>
<include name="dr/app/util/**/*.class"/>
<include name="dr/app/java16compat/**/*.class"/>
<include name="dr/evolution/alignment/**/*.class"/>
<include name="dr/evolution/coalescent/**/*.class"/>
<include name="dr/evolution/colouring/**/*.class"/>
<include name="dr/evolution/datatype/**/*.class"/>
<include name="dr/evolution/distance/**/*.class"/>
<include name="dr/evolution/io/**/*.class"/>
<include name="dr/evolution/parsimony/**/*.class"/>
<include name="dr/evolution/sequence/**/*.class"/>
<include name="dr/evolution/tree/**/*.class"/>
<include name="dr/evolution/util/**/*.class"/>
<include name="dr/gui/chart/**/*.class"/>
<include name="dr/inference/**/*.class"/>
<include name="dr/math/**/*.class"/>
<include name="dr/matrix/**/*.class"/>
<include name="dr/stats/**/*.class"/>
<include name="dr/util/**/*.class"/>
<include name="dr/xml/**/*.class"/>
</fileset>
<fileset dir="${src}">
<include name="dr/app/tracer/**/*.png"/>
<include name="dr/app/tracer/**/*.gif"/>
<include name="dr/app/tracer/**/*.tiff"/>
<include name="org/virion/jam/**/*.png"/>
</fileset>
<zipgroupfileset dir="${lib}" includes="jebl.jar"/>
<zipgroupfileset dir="${lib}" includes="jam.jar"/>
<zipgroupfileset dir="${lib}" includes="itext-1.4.5.jar"/>
<zipgroupfileset dir="${lib}" includes="commons-math-2.2.jar"/>
</jar>
</target>
<property name="version" value="1.6.1pre" />
<property name="version_number" value="1.6.1" />
<property name="release_dir" value="release_tracer" />
<property name="name" value="Tracer" />
<property name="packaging_tools" value="packaging_tools" />
<property name="common_dir" value="${release_dir}/common" />
<property name="Mac_dir" value="${release_dir}/Mac" />
<property name="Linux_dir" value="${release_dir}/Linux" />
<property name="Windows_dir" value="${release_dir}/Windows" />
<property name="Mac_package_dir" value="${Mac_dir}/${name} v${version}" />
<property name="Linux_package_dir" value="${Linux_dir}/${name}_v${version}" />
<property name="Windows_package_dir" value="${Windows_dir}/${name} v${version}" />
<!-- Need to either install Launch4j under {BEAST workspace}/${release}
or install it in the default directory and change the location of launch4j.dir -->
<target name="windows" depends="dist" description="release Windows version of Tracer">
<delete dir="${Windows_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Windows_package_dir}" />
<property name="launch4j.dir" location="${Windows_dir}/launch4j" />
<taskdef name="launch4j" classname="net.sf.launch4j.ant.Launch4jTask"
classpath="${launch4j.dir}/launch4j.jar :${launch4j.dir}/lib/xstream.jar" />
<copy file="${dist}/tracer.jar" todir="${Windows_package_dir}/lib"/>
<copy todir="${Windows_package_dir}/lib">
<fileset dir="${Windows_dir}/lib"/>
</copy>
<copy file="${common_dir}/README.txt" todir="${Windows_package_dir}"/>
<launch4j configFile="${Windows_dir}/tracer_launch4j.xml"
jar="${dist}/tracer.jar"
outfile="${Windows_package_dir}/${name} v${version}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}"/>
<zip destfile="${release_dir}/${name} v${version}.zip">
<zipfileset dir="${Windows_package_dir}" prefix="${name} v${version}"/>
</zip>
<echo message="Windows version release is finished." />
</target>
<target name="linux" description="release Linux/Unix version of Tracer">
<delete dir="${Linux_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Linux_package_dir}" />
<copy todir="${Linux_package_dir}/bin">
<fileset dir="${Linux_dir}/scripts"/>
</copy>
<chmod dir="${Linux_package_dir}/bin" perm="755" includes="**/**"/>
<copy file="${Linux_dir}/icons/Tracer.png" todir="${Linux_package_dir}/images"/>
<copy file="${dist}/tracer.jar" todir="${Linux_package_dir}/lib"/>
<copy todir="${Linux_package_dir}/lib">
<fileset dir="${Linux_dir}/lib"/>
</copy>
<copy file="${common_dir}/README.txt" todir="${Linux_package_dir}"/>
<tar destfile="${release_dir}/${name}_v${version}.tgz" compression="gzip">
<tarfileset dir="${Linux_package_dir}" prefix="${name}_v${version}"/>
</tar>
<echo message="Linux/Unix version release is finished." />
</target>
<target name="mac" description="release Mac version of Tracer">
<delete dir="${Mac_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Mac_package_dir}" />
<copy file="${common_dir}/README.txt" todir="${Mac_package_dir}"/>
<taskdef name="jarbundler" classname="net.sourceforge.jarbundler.JarBundler"/>
<!-- create a jar bundle for the mac -->
<jarbundler dir="${Mac_package_dir}"
name="${name} v${version}"
mainclass="dr.app.tracer.application.TracerApp"
stubfile="${packaging_tools}/mac/universalJavaApplicationStub"
useJavaXKey="true"
icon="${Mac_dir}/icons/Tracer.icns"
jvmversion="1.6+"
vmoptions="-Xmx1024M"
arguments=""
version="${version}"
copyright="${name} v${version}, Copyright 2003-2015, Andrew Rambaut, Marc Suchard &amp; Alexei J. Drummond"
bundleid="tracer" >
<javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
<jarfileset dir="${dist}">
<include name="**/tracer.jar"/>
</jarfileset>
<jarfileset dir="${Mac_dir}/lib">
<include name="**/quaqua.jar"/>
</jarfileset>
<jarfileset dir="${Mac_dir}/lib">
<include name="libquaqua*.jnilib"/>
</jarfileset>
</jarbundler>
<echo message="Building disk image." />
<!-- create disk image -->
<exec executable="/usr/bin/hdiutil">
<arg value="create"/>
<arg value="-ov"/>
<arg value="-srcfolder"/>
<arg value="${Mac_package_dir}"/>
<arg value="-volname"/>
<arg value="${name} v${version}"/>
<arg value="-imagekey"/>
<arg value="zlib-level=6"/>
<arg value="${release_dir}/${name} v${version}.dmg"/>
</exec>
<echo message="Mac version release is finished." />
</target>
</project>
debian/changelog
View file @ 93200f9e
beast-mcmc (1.10.0+dfsg-1) UNRELEASED; urgency=medium
* New upstream version
* Exclude Latex doc creation
* New Build-Depends: libejml-java
* New versioned Build-Depends: libhmsbeagle-java (>= 2.1.2+git20180619)
-- Andreas Tille <tille@debian.org> Thu, 21 Jun 2018 17:50:40 +0200
beast-mcmc (1.8.4+dfsg.1-3) unstable; urgency=medium
[ Steffen Moeller ]
......
debian/control
View file @ 93200f9e
......@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11~),
libjam-java (>= 0.1.20140824),
figtree,
liboptions-java,
libhmsbeagle-java (>= 2.1.2+20150609),
libhmsbeagle-java (>= 2.1.2+git20180619),
libcolt-free-java,
libmpj-java,
r-cran-rjava,
......@@ -22,9 +22,8 @@ Build-Depends: debhelper (>= 11~),
junit4,
libmtj-java,
libitext1-java,
texlive-latex-base,
texlive-latex-extra,
texlive-fonts-recommended
libejml-java,
libjlapack-java
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/beast-mcmc
Vcs-Git: https://salsa.debian.org/med-team/beast-mcmc.git
......
debian/patches/fix_classpath_in_build_tracer_xml.patch deleted 100644 → 0
View file @ a00c73da
Author: Andreas Tille <tille@debian.org>
Date: Tue, 10 Jan 2012 22:29:24 +0100
Description: Make sure also tracer is builded with Debian packages JARs
--- a/build_tracer.xml
+++ b/build_tracer.xml
@@ -32,6 +32,7 @@
<property name="src" location="src"/>
<property name="build" location="build"/>
<property name="lib" location="lib"/>
+ <property name="deblib" location="/usr/share/java" />
<property name="dist" location="dist"/>
<property environment="env"/>
@@ -56,7 +57,7 @@
<target name="compile-basic" depends="init">
<!-- Compile the java code from ${src} into ${build} -->
<javac source="1.6" target="1.6" srcdir="${src}" destdir="${build}"
- classpath="${lib}/colt.jar:${lib}/commons-math-2.2.jar:${lib}/jebl.jar:${lib}/jam.jar:${lib}/itext-1.4.5.jar:${lib}/jdom.jar:${lib}/mtj.jar:${lib}/JRI.jar:${lib}/mpj.jar">
+ classpath="${deblib}/colt.jar:${deblib}/commons-math-2.2.jar:${deblib}/jebl.jar:${deblib}/jam.jar:${deblib}/itext-1.4.5.jar:${deblib}/jdom.jar:${deblib}/mtj.jar:${deblib}/JRI.jar:${deblib}/mpj.jar">
<include name="dr/app/tracer/**"/>
<include name="dr/app/util/**"/>
<include name="dr/app/gui/**"/>
@@ -121,10 +122,10 @@
<include name="dr/app/tracer/**/*.tiff"/>
<include name="org/virion/jam/**/*.png"/>
</fileset>
- <zipgroupfileset dir="${lib}" includes="jebl.jar"/>
- <zipgroupfileset dir="${lib}" includes="jam.jar"/>
- <zipgroupfileset dir="${lib}" includes="itext-1.4.5.jar"/>
- <zipgroupfileset dir="${lib}" includes="commons-math-2.2.jar"/>
+ <zipgroupfileset dir="${deblib}" includes="jebl.jar"/>
+ <zipgroupfileset dir="${deblib}" includes="jam.jar"/>
+ <zipgroupfileset dir="${deblib}" includes="itext-1.4.5.jar"/>
+ <zipgroupfileset dir="${deblib}" includes="commons-math.jar"/>
</jar>
</target>
@@ -137,46 +138,12 @@
<property name="packaging_tools" value="packaging_tools" />
<property name="common_dir" value="${release_dir}/common" />
- <property name="Mac_dir" value="${release_dir}/Mac" />
<property name="Linux_dir" value="${release_dir}/Linux" />
- <property name="Windows_dir" value="${release_dir}/Windows" />
- <property name="Mac_package_dir" value="${Mac_dir}/${name} v${version}" />
<property name="Linux_package_dir" value="${Linux_dir}/${name}_v${version}" />
- <property name="Windows_package_dir" value="${Windows_dir}/${name} v${version}" />
<!-- Need to either install Launch4j under {BEAST workspace}/${release}
or install it in the default directory and change the location of launch4j.dir -->
- <target name="windows" depends="dist" description="release Windows version of Tracer">
-
- <delete dir="${Windows_package_dir}" />
- <!-- Create the release directory -->
- <mkdir dir="${Windows_package_dir}" />
-
- <property name="launch4j.dir" location="${Windows_dir}/launch4j" />
- <taskdef name="launch4j" classname="net.sf.launch4j.ant.Launch4jTask"
- classpath="${launch4j.dir}/launch4j.jar :${launch4j.dir}/lib/xstream.jar" />
-
- <copy file="${dist}/tracer.jar" todir="${Windows_package_dir}/lib"/>
- <copy todir="${Windows_package_dir}/lib">
- <fileset dir="${Windows_dir}/lib"/>
- </copy>
- <copy file="${common_dir}/README.txt" todir="${Windows_package_dir}"/>
-
- <launch4j configFile="${Windows_dir}/tracer_launch4j.xml"
- jar="${dist}/tracer.jar"
- outfile="${Windows_package_dir}/${name} v${version}.exe"
- fileVersion="${version_number}.0"
- txtFileVersion="${version}"
- productVersion="${version_number}.0"
- txtProductVersion="${version}"/>
-
- <zip destfile="${release_dir}/${name} v${version}.zip">
- <zipfileset dir="${Windows_package_dir}" prefix="${name} v${version}"/>
- </zip>
-
- <echo message="Windows version release is finished." />
- </target>
<target name="linux" description="release Linux/Unix version of Tracer">
<delete dir="${Linux_package_dir}" />
@@ -203,56 +170,4 @@
<echo message="Linux/Unix version release is finished." />
</target>
- <target name="mac" description="release Mac version of Tracer">
- <delete dir="${Mac_package_dir}" />
- <!-- Create the release directory -->
- <mkdir dir="${Mac_package_dir}" />
-
- <copy file="${common_dir}/README.txt" todir="${Mac_package_dir}"/>
-
- <taskdef name="jarbundler" classname="net.sourceforge.jarbundler.JarBundler"/>
-
- <!-- create a jar bundle for the mac -->
- <jarbundler dir="${Mac_package_dir}"
- name="${name} v${version}"
- mainclass="dr.app.tracer.application.TracerApp"
- stubfile="${packaging_tools}/mac/universalJavaApplicationStub"
- useJavaXKey="true"
- icon="${Mac_dir}/icons/Tracer.icns"
- jvmversion="1.6+"
- vmoptions="-Xmx1024M"
- arguments=""
- version="${version}"
- copyright="${name} v${version}, Copyright 2003-2015, Andrew Rambaut, Marc Suchard &amp; Alexei J. Drummond"
- bundleid="tracer" >
- <javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
- <jarfileset dir="${dist}">
- <include name="**/tracer.jar"/>
- </jarfileset>
- <jarfileset dir="${Mac_dir}/lib">
- <include name="**/quaqua.jar"/>
- </jarfileset>
- <jarfileset dir="${Mac_dir}/lib">
- <include name="libquaqua*.jnilib"/>
- </jarfileset>
- </jarbundler>
-
- <echo message="Building disk image." />
-
- <!-- create disk image -->
- <exec executable="/usr/bin/hdiutil">
- <arg value="create"/>
- <arg value="-ov"/>
- <arg value="-srcfolder"/>
- <arg value="${Mac_package_dir}"/>
- <arg value="-volname"/>
- <arg value="${name} v${version}"/>
- <arg value="-imagekey"/>
- <arg value="zlib-level=6"/>
- <arg value="${release_dir}/${name} v${version}.dmg"/>
- </exec>
-
- <echo message="Mac version release is finished." />
- </target>
-
</project>
debian/patches/fix_classpath_in_build_xml.patch
View file @ 93200f9e
......@@ -5,7 +5,7 @@ Description: Make sure package builds with Debian packages JARs
Forwarded: no
--- a/build.xml
+++ b/build.xml
@@ -36,6 +36,7 @@
@@ -37,6 +37,7 @@
<property name="src" location="src"/>
<property name="build" location="build"/>
<property name="lib" location="lib"/>
......@@ -13,7 +13,7 @@ Forwarded: no
<property name="dist" location="${build}/dist"/>
<property name="main_class_BEAST" value="dr.app.beast.BeastMain"/>
@@ -47,6 +48,19 @@
@@ -48,6 +49,21 @@
<path id="classpath">
<fileset dir="${lib}" includes="**/*.jar"/>
......@@ -30,10 +30,12 @@ Forwarded: no
+ <fileset dir="${deblib}" includes="mpj.jar"/>
+ <fileset dir="${deblib}" includes="mtj.jar"/>
+ <fileset dir="${deblib}" includes="options.jar"/>
+ <fileset dir="${deblib}" includes="EJML.jar"/>
+ <fileset dir="${deblib}" includes="jlapack-lapack.jar"/>
</path>
<!-- start -->
@@ -159,14 +173,6 @@
@@ -159,17 +175,6 @@
<include name="org/virion/jam/**/*.png"/>
<include name="dr/**/*.properties"/>
</fileset>
......@@ -45,10 +47,13 @@ Forwarded: no
- <zipgroupfileset dir="${lib}" includes="JRI.jar"/>
- <zipgroupfileset dir="${lib}" includes="colt.jar"/>
- <zipgroupfileset dir="${lib}" includes="beagle.jar"/>
- <zipgroupfileset dir="${lib}" includes="beagle.jar"/>
- <zipgroupfileset dir="${lib}" includes="EJML-core-0.30.jar"/>
- <zipgroupfileset dir="${lib}" includes="EJML-dense64-0.30.jar"/>
</jar>
<!-- Put everything in ${build} into the beauti.jar file -->
@@ -222,11 +228,6 @@
@@ -226,11 +231,6 @@
<fileset dir="${src}">
<include name="dr/**/*.png"/>
</fileset>
......@@ -59,10 +64,10 @@ Forwarded: no
- <zipgroupfileset dir="${lib}" includes="mtj.jar"/>
</jar>
</target>
<!-- Put everything in ${build} into the trace.jar file -->
--- a/.classpath
+++ b/.classpath
@@ -1,20 +1,16 @@
@@ -1,20 +1,18 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" path="src"/>
......@@ -92,5 +97,7 @@ Forwarded: no
+ <classpathentry kind="lib" path="/usr/share/java/mpj.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/mtj.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/commons-math.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/EJML.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/jlapack-lapack.jar"/>
<classpathentry kind="output" path="bin"/>
</classpath>
debian/patches/fix_encoding.patch
View file @ 93200f9e
......@@ -4,16 +4,7 @@ Description: Fix encoding issue
--- a/src/dr/app/beauti/components/discrete/DiscreteTraitsComponentGenerator.java
+++ b/src/dr/app/beauti/components/discrete/DiscreteTraitsComponentGenerator.java
@@ -259,7 +259,7 @@ public class DiscreteTraitsComponentGene
}
- if (model.isActivateBSSVS()) // If "BSSVS" is not activated, rateIndicator should not b§e there.
+ if (model.isActivateBSSVS()) // If "BSSVS" is not activated, rateIndicator should not be there.
writeStatisticModel(model, writer);
}
@@ -494,4 +494,4 @@ public class DiscreteTraitsComponentGene
@@ -716,4 +716,4 @@ public class DiscreteTraitsComponentGene
}
}
......
debian/patches/patch_tex_docs.patch deleted 100644 → 0
View file @ a00c73da
Description: Fix some latex error that are preventing proper creation of docs
Author: Andreas Tille <tille@debian.org>
Date: Tue, 05 Jun 2012 14:38:11 +0200
LastUpdated: Mon, 17 Dec 2012 16:43:17 +0100
--- a/doc/Yule.tex
+++ b/doc/Yule.tex
@@ -35,6 +35,7 @@
\begin{document}
\title{\textbf{The Yule model}}
+\date{22. May, 2007}
\author{\textsc{Alexei J. Drummond}}
--- a/doc/BookSection/BookSection.tex
+++ b/doc/BookSection/BookSection.tex
@@ -1,7 +1,7 @@
\NeedsTeXFormat{LaTeX2e}[1996/06/01]
-\documentclass[cup7b, english]{cupbook}
+\documentclass[english]{report}
\usepackage{graphicx}
@@ -32,6 +32,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands.
\title{The Phylogenetics Handbook}
+\date{September 14, 2007}
\makeatother
\begin{document}
--- a/doc/SerialSampleCoalescent.tex
+++ b/doc/SerialSampleCoalescent.tex
@@ -33,7 +33,7 @@
\begin{document}
\title{\textbf{The serially-sampled coalescent}}
-
+\date{July 12, 2007}
\author{\textsc{Alexei J. Drummond}}
\maketitle
--- a/doc/BEAST14_Manual.tex
+++ b/doc/BEAST14_Manual.tex
@@ -35,7 +35,7 @@
\begin{document}
\title{\textbf{A Rough Guide to BEAST 1.4}}
-
+\date{July 6, 2007}
\author{\textsc{Alexei J. Drummond}$^{1}$, \textsc{Simon Y.W. Ho},\\
\textsc{Nic Rawlence} and \textsc{Andrew Rambaut}$^{2}$\\
--- a/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex
+++ b/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex
@@ -789,7 +789,7 @@ Define the prior not specified (marked a
\medskip{}
-\includegraphics[scale=0.4]{figures3/BEAUti_Prior}
+\includegraphics[scale=0.4]{figures3/BEAUTi_Prior}
\medskip{}
debian/patches/series
View file @ 93200f9e
enable_hardening.patch
fix_classpath_in_build_xml.patch
patch_tex_docs.patch
fix_classpath_in_build_tracer_xml.patch
create_soname.patch
fix_encoding.patch
tex_encoding.patch
debian/patches/tex_encoding.patch deleted 100644 → 0
View file @ a00c73da
Description: Fix encoding issues that caused FTBFS with TeX Live 2018
Author: Adrian Bunk <bunk@debian.org>
Bug-Debian: https://bugs.debian.org/896483
--- beast-mcmc-1.8.4+dfsg.1.orig/doc/BEAST14_Manual.tex
+++ beast-mcmc-1.8.4+dfsg.1/doc/BEAST14_Manual.tex
@@ -1,6 +1,7 @@
%% LyX 1.4.3 created this file. For more info, see http://www.lyx.org/.
%% Do not edit unless you really know what you are doing.
\documentclass[a4paper, english]{article}
+ \usepackage[latin1]{inputenc}
\usepackage{graphicx}
\usepackage{amssymb}
\usepackage{epstopdf}
--- beast-mcmc-1.8.4+dfsg.1.orig/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex
+++ beast-mcmc-1.8.4+dfsg.1/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex
@@ -1,4 +1,6 @@
\documentclass[12pt]{article}
+\usepackage[latin1]{inputenc}
+\usepackage[T1]{fontenc}
\usepackage{graphicx}
\usepackage[left=3cm,top=3cm,right=3cm,bottom=3cm]{geometry}
debian/rules
View file @ 93200f9e
......@@ -13,7 +13,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
JAVA_HOME := /usr/lib/jvm/default-java
DEBJAR := /usr/share/java
CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:$(JAVA_HOME)/lib/tools.jar:$(DEBJAR)/beagle.jar:$(DEBJAR)/mpj.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:$(DEBJAR)/options.jar:$(DEBJAR)/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar
CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:$(JAVA_HOME)/lib/tools.jar:$(DEBJAR)/beagle.jar:$(DEBJAR)/mpj.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:$(DEBJAR)/options.jar:$(DEBJAR)/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:$(DEBJAR)/EJML.jar:$(DEBJAR)/jlapack-lapack.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar
# to run the test suite
JAVA := $(JAVA_HOME)/bin/java
......@@ -26,6 +26,7 @@ ANT_ARGS := -Dcompile.debug=true -Dcompile.optimize=true
override_dh_auto_clean:
rm -f native/*\.o native/*\.so native/*\.so\.*
ifeq ($(HASTEXDOC),yes)
for cleantex in \
Practical_BEAST \
BookSection \
......@@ -36,6 +37,7 @@ override_dh_auto_clean:
; do \
find doc -not -name "*.tex" -a -not -name "*.bib" -and -name "$${cleantex}.*" -exec rm -f \{\} \; ; \
done
endif
ant clean
CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
......@@ -53,6 +55,7 @@ override_dh_auto_build:
# gcc -shared -Wl,-soname,libNucleotideLikelihoodCore.so.0 -o libNucleotideLikelihoodCore.so.0 libNucleotideLikelihoodCore.o -lc ; \
# gcc $(CFLAGS) $(LDFLAGS) -Wall -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ AminoAcidLikelihoodCore.c -o libAminoAcidLikelihoodCore.o ; \
# gcc -shared -Wl,-soname,libAminoAcidLikelihoodCore.so.0 -o libAminoAcidLikelihoodCore.so libAminoAcidLikelihoodCore.o -lc
ifeq ($(HASTEXDOC),yes)
#
# Build extra LaTeX documentation
#
......@@ -61,7 +64,9 @@ override_dh_auto_build:
cd doc; $(PDFLATEX) Yule.tex; $(PDFLATEX) Yule.tex
cd doc; $(PDFLATEX) SerialSampleCoalescent.tex; $(PDFLATEX) SerialSampleCoalescent.tex
cd doc; $(PDFLATEX) BEAST14_Manual.tex; $(PDFLATEX) BEAST14_Manual.tex
#
endif
override_dh_auto_test:
#####################################################################
## Run test suite ##
## -------------- ##
......
doc/BEAST.bib deleted 100755 → 0
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doc/BEAST14.tex deleted 100755 → 0
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