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.classpath deleted 100644 → 0
View file @ 1ffe4cf3
<?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>
.gitignore
View file @ 694dc530
......@@ -4,5 +4,8 @@
/META-INF
/out
# Eclipse ignores
/.classpath
# OS X ignores
.DS_Store
Dockerfile
View file @ 694dc530
......@@ -32,9 +32,9 @@ RUN chmod 600 /root/.vnc/passwd
# Install BEAGLE
RUN apt-get update && apt-get install -y build-essential autoconf automake libtool pkg-config
RUN cd /root && git clone --depth=1 https://github.com/beagle-dev/beagle-lib.git
# use latest release v3.0.1, issue #786
RUN cd /root && git clone --branch v3.0.1 --depth=1 https://github.com/beagle-dev/beagle-lib.git
RUN cd /root/beagle-lib && ./autogen.sh && ./configure --prefix=/usr/local && make install
ENV LD_LIBRARY_PATH=/lib:/usr/lib:/usr/local/lib
RUN ldconfig
# Ant build fails if the repo dir isn't named beast2
......
README.md
View file @ 694dc530
......@@ -24,7 +24,7 @@ Development Rules and Philosophy
Aspects relating to BEAST 2 development such as coding style, version
numbering and design philosophy are discussed on the BEAST 2 web page at
http://beast2.org/core-development-rules/.
http://www.beast2.org/package-development-guide/core-development-rules/.
License
-------
......@@ -32,7 +32,8 @@ License
BEAST 2 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 2.1 of the License, or
(at your option) any later version.
(at your option) any later version. A copy of the license is contained
in the file COPYING, located in the root directory of this repository.
This software is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
......
build.xml
View file @ 694dc530
......@@ -256,8 +256,8 @@
<!-- Release -->
<property name="version" value="2.5.0" />
<property name="version_number" value="2.5.0" />
<property name="version" value="2.5.1" />
<property name="version_number" value="2.5.1" />
<property name="release_dir" value="release" />
<property name="copyright" value="Beast 2 development team 2011-2018" />
......@@ -929,7 +929,7 @@
<mkdir dir="${Mac_package_dir}" />
<copy todir="${Mac_package_dir}/bin">
<fileset dir="${Linux_dir}/bin" />
<fileset dir="${Linux_dir}/jrebin" />
</copy>
<chmod dir="${Mac_package_dir}/bin" perm="755" includes="**/**" />
......@@ -941,7 +941,10 @@
</fileset>
</copy>
<exec executable="cp">
<arg line="-R ../jre1.8.0_161.jre ${Mac_package_dir}/jre1.8.0_161.jre"/>
<arg line="-R ../jre1.8.0_161.jre/Contents/Home ${Mac_package_dir}/jre1.8.0_161"/>
</exec>
<exec executable="gcc">
<arg line="release/Mac/launch.c -o JavaAppLauncher"/>
</exec>
<!--copy todir="${Mac_package_dir}/doc">
<fileset dir="${common_dir}/doc" />
......@@ -983,6 +986,9 @@
<argument value="-working"/>
<argument value="-options"/>
</bundleapp>
<delete file="${Mac_package_dir}/BEAST.app/Contents/MacOS/JavaAppLauncher"/>
<copy file="JavaAppLauncher" todir="${Mac_package_dir}/BEAST.app/Contents/MacOS/"/>
<chmod dir="${Mac_package_dir}/BEAST.app/Contents/MacOS/" perm="755" includes="JavaAppLauncher"/>
<exec executable="codesign">
<arg value="--deep"/>
......@@ -1011,6 +1017,9 @@
<option value="-Duser.language=en"/>
<argument value="-capture"/>
</bundleapp>
<delete file="${Mac_package_dir}/BEAUti.app/Contents/MacOS/JavaAppLauncher"/>
<copy file="JavaAppLauncher" todir="${Mac_package_dir}/BEAUti.app/Contents/MacOS/"/>
<chmod dir="${Mac_package_dir}/BEAUti.app/Contents/MacOS/" perm="755" includes="JavaAppLauncher"/>
<exec executable="codesign">
<arg value="--deep"/>
......@@ -1037,6 +1046,9 @@
<option value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>
<option value="-Duser.language=en"/>
</bundleapp>
<delete file="${Mac_package_dir}/LogCombiner.app/Contents/MacOS/JavaAppLauncher"/>
<copy file="JavaAppLauncher" todir="${Mac_package_dir}/LogCombiner.app/Contents/MacOS/"/>
<chmod dir="${Mac_package_dir}/LogCombiner.app/Contents/MacOS/" perm="755" includes="JavaAppLauncher"/>
<exec executable="codesign">
<arg value="--deep"/>
......@@ -1063,6 +1075,9 @@
<option value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>
<option value="-Duser.language=en"/>
</bundleapp>
<delete file="${Mac_package_dir}/TreeAnnotator.app/Contents/MacOS/JavaAppLauncher"/>
<copy file="JavaAppLauncher" todir="${Mac_package_dir}/TreeAnnotator.app/Contents/MacOS/"/>
<chmod dir="${Mac_package_dir}/TreeAnnotator.app/Contents/MacOS/" perm="755" includes="JavaAppLauncher"/>
<exec executable="codesign">
<arg value="--deep"/>
......@@ -1088,6 +1103,9 @@
<option value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>
<option value="-Duser.language=en"/>
</bundleapp>
<delete file="${Mac_package_dir}/DensiTree.app/Contents/MacOS/JavaAppLauncher"/>
<copy file="JavaAppLauncher" todir="${Mac_package_dir}/DensiTree.app/Contents/MacOS/"/>
<chmod dir="${Mac_package_dir}/DensiTree.app/Contents/MacOS/" perm="755" includes="JavaAppLauncher"/>
<exec executable="codesign">
<arg value="-s"/>
......@@ -1113,6 +1131,9 @@
<option value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>
<option value="-Duser.language=en"/>
</bundleapp>
<delete file="${Mac_package_dir}/AppLauncher.app/Contents/MacOS/JavaAppLauncher"/>
<copy file="JavaAppLauncher" todir="${Mac_package_dir}/AppLauncher.app/Contents/MacOS/"/>
<chmod dir="${Mac_package_dir}/AppLauncher.app/Contents/MacOS/" perm="755" includes="JavaAppLauncher"/>
<exec executable="codesign">
<arg value="--deep"/>
......
debian/changelog
View file @ 694dc530
beast2-mcmc (2.5.0+dfsg-1) unstable; urgency=medium
beast2-mcmc (2.5.1+dfsg-1) UNRELEASED; urgency=medium
[ Steffen Moeller ]
* d/u/metadata:
......@@ -13,9 +13,9 @@ beast2-mcmc (2.5.0+dfsg-1) unstable; 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
* Standards-Version: 4.2.1
-- Andreas Tille <tille@debian.org> Thu, 19 Jul 2018 08:20:21 +0200
-- Andreas Tille <tille@debian.org> Mon, 15 Oct 2018 10:03:36 +0200
beast2-mcmc (2.4.4+dfsg-1) unstable; urgency=medium
......
debian/control
View file @ 694dc530
......@@ -17,7 +17,7 @@ Build-Depends: debhelper (>= 11~),
junit4,
texlive-latex-base,
texlive-latex-extra
Standards-Version: 4.1.4
Standards-Version: 4.2.1
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/revert_NewickLexer.java_to_antlr_4.5.patch 0 → 100644
View file @ 694dc530
--- src/beast/util/treeparser/NewickLexer.java 2018-07-19 13:58:48.796079607 +0200
+++ /home/andreas/debian-maintain/salsa/med-team/beast2-mcmc_new-file/NewickLexer.java 2018-07-19 14:42:21.968042914 +0200
@@ -1,4 +1,4 @@
-// Generated from NewickLexer.g4 by ANTLR 4.5
+// Generated from /Users/vaughant/code/beast_and_friends/beast2/src/beast/util/treeparser/NewickLexer.g4 by ANTLR 4.7
package beast.util.treeparser;
import org.antlr.v4.runtime.Lexer;
import org.antlr.v4.runtime.CharStream;
@@ -11,7 +11,7 @@
@SuppressWarnings({"all", "warnings", "unchecked", "unused", "cast"})
public class NewickLexer extends Lexer {
- static { RuntimeMetaData.checkVersion("4.5", RuntimeMetaData.VERSION); }
+ static { RuntimeMetaData.checkVersion("4.7", RuntimeMetaData.VERSION); }
protected static final DFA[] _decisionToDFA;
protected static final PredictionContextCache _sharedContextCache =
@@ -90,9 +90,6 @@
public String getGrammarFileName() { return "NewickLexer.g4"; }
@Override
- public String[] getChannelNames() { return channelNames; }
-
- @Override
public String[] getRuleNames() { return ruleNames; }
@Override
debian/patches/reverted_to_antlr_4.5_deacdc96.patch 0 → 100644
View file @ 694dc530
Origin: https://github.com/CompEvol/beast2/commit/deacdc96.patch
From: Tim Vaughan <tgvaughan@gmail.com>
Date: Tue, 16 Jan 2018 14:24:37 +0100
Subject: [PATCH] Revert "Reverted to ANTLR 4.5, as per issue #744."
Remark: by Andreas Tille <tille@debian.org>
Most of the original patch was applied in current upstream tarball
this are the remaining changes that were in the diff
This reverts commit 8a1f3addbeb5f016a0b5c8f7fb634227452d0175.
---
build.xml | 4 +-
lib/antlr-runtime-4.5.jar | Bin 374042 -> 0 bytes
lib/antlr-runtime-4.7.jar | Bin 0 -> 334662 bytes
src/beast/util/TreeParser.java | 10 ++---
src/beast/util/treeparser/NewickLexer.java | 32 ++++++++++------
src/beast/util/treeparser/NewickParser.java | 42 ++++++++++++++-------
.../util/treeparser/NewickParserBaseListener.java | 3 +-
.../util/treeparser/NewickParserBaseVisitor.java | 3 +-
.../util/treeparser/NewickParserListener.java | 3 +-
src/beast/util/treeparser/NewickParserVisitor.java | 3 +-
10 files changed, 59 insertions(+), 41 deletions(-)
delete mode 100644 lib/antlr-runtime-4.5.jar
create mode 100644 lib/antlr-runtime-4.7.jar
--- a/build.xml
+++ b/build.xml
@@ -143,7 +143,7 @@
<zipgroupfileset dir="${lib}" includes="beagle.jar" />
<zipgroupfileset dir="${lib}" includes="colt.jar" />
<zipgroupfileset dir="${lib}" includes="commons-math3-3.1.1.jar" />
- <zipgroupfileset dir="${lib}" includes="antlr-runtime-4.7.jar"/>
+ <zipgroupfileset dir="${lib}" includes="antlr-runtime-4.5.jar"/>
</jar>
<jar jarfile="${dist}/launcher.jar">
<fileset dir="${build}">
--- a/src/beast/util/treeparser/NewickLexer.java
+++ b/src/beast/util/treeparser/NewickLexer.java
@@ -1,4 +1,4 @@
-// Generated from /Users/vaughant/code/beast_and_friends/beast2/src/beast/util/treeparser/NewickLexer.g4 by ANTLR 4.7
+// Generated from NewickLexer.g4 by ANTLR 4.5
package beast.util.treeparser;
import org.antlr.v4.runtime.Lexer;
import org.antlr.v4.runtime.CharStream;
@@ -11,7 +11,7 @@ import org.antlr.v4.runtime.misc.*;
@SuppressWarnings({"all", "warnings", "unchecked", "unused", "cast"})
public class NewickLexer extends Lexer {
- static { RuntimeMetaData.checkVersion("4.7", RuntimeMetaData.VERSION); }
+ static { RuntimeMetaData.checkVersion("4.5", RuntimeMetaData.VERSION); }
protected static final DFA[] _decisionToDFA;
protected static final PredictionContextCache _sharedContextCache =
@@ -90,6 +90,9 @@ public class NewickLexer extends Lexer {
public String getGrammarFileName() { return "NewickLexer.g4"; }
@Override
+ public String[] getChannelNames() { return channelNames; }
+
+ @Override
public String[] getRuleNames() { return ruleNames; }
@Override
@@ -216,4 +219,4 @@ public class NewickLexer extends Lexer {
_decisionToDFA[i] = new DFA(_ATN.getDecisionState(i), i);
}
}
-}
\ No newline at end of file
+}
--- a/src/beast/util/treeparser/NewickParserVisitor.java
+++ b/src/beast/util/treeparser/NewickParserVisitor.java
@@ -1,4 +1,4 @@
-// Generated from NewickParser.g4 by ANTLR 4.7
+// Generated from NewickParser.g4 by ANTLR 4.5
package beast.util.treeparser;
import org.antlr.v4.runtime.tree.ParseTreeVisitor;
@@ -70,4 +70,4 @@ public interface NewickParserVisitor<T>
* @return the visitor result
*/
T visitVector(NewickParser.VectorContext ctx);
-}
\ No newline at end of file
+}
--- a/src/beast/util/treeparser/NewickParser.java
+++ b/src/beast/util/treeparser/NewickParser.java
@@ -1,4 +1,4 @@
-// Generated from NewickParser.g4 by ANTLR 4.7
+// Generated from NewickParser.g4 by ANTLR 4.5
package beast.util.treeparser;
import org.antlr.v4.runtime.atn.*;
import org.antlr.v4.runtime.dfa.DFA;
@@ -11,7 +11,7 @@ import java.util.ArrayList;
@SuppressWarnings({"all", "warnings", "unchecked", "unused", "cast"})
public class NewickParser extends Parser {
- static { RuntimeMetaData.checkVersion("4.7", RuntimeMetaData.VERSION); }
+ static { RuntimeMetaData.checkVersion("4.5", RuntimeMetaData.VERSION); }
protected static final DFA[] _decisionToDFA;
protected static final PredictionContextCache _sharedContextCache =
@@ -795,4 +795,4 @@ public class NewickParser extends Parser
_decisionToDFA[i] = new DFA(_ATN.getDecisionState(i), i);
}
}
-}
\ No newline at end of file
+}
--- a/src/beast/util/treeparser/NewickParserListener.java
+++ b/src/beast/util/treeparser/NewickParserListener.java
@@ -1,4 +1,4 @@
-// Generated from NewickParser.g4 by ANTLR 4.7
+// Generated from NewickParser.g4 by ANTLR 4.5
package beast.util.treeparser;
import org.antlr.v4.runtime.tree.ParseTreeListener;
@@ -107,4 +107,4 @@ public interface NewickParserListener ex
* @param ctx the parse tree
*/
void exitVector(NewickParser.VectorContext ctx);
-}
\ No newline at end of file
+}
--- a/src/beast/util/treeparser/NewickParserBaseListener.java
+++ b/src/beast/util/treeparser/NewickParserBaseListener.java
@@ -1,4 +1,4 @@
-// Generated from NewickParser.g4 by ANTLR 4.7
+// Generated from NewickParser.g4 by ANTLR 4.5
package beast.util.treeparser;
import org.antlr.v4.runtime.ParserRuleContext;
@@ -156,4 +156,4 @@ public class NewickParserBaseListener im
* <p>The default implementation does nothing.</p>
*/
@Override public void visitErrorNode(ErrorNode node) { }
-}
\ No newline at end of file
+}
--- a/src/beast/util/treeparser/NewickParserBaseVisitor.java
+++ b/src/beast/util/treeparser/NewickParserBaseVisitor.java
@@ -1,4 +1,4 @@
-// Generated from NewickParser.g4 by ANTLR 4.7
+// Generated from NewickParser.g4 by ANTLR 4.5
package beast.util.treeparser;
import org.antlr.v4.runtime.tree.AbstractParseTreeVisitor;
@@ -81,4 +81,4 @@ public class NewickParserBaseVisitor<T>
* {@link #visitChildren} on {@code ctx}.</p>
*/
@Override public T visitVector(NewickParser.VectorContext ctx) { return visitChildren(ctx); }
-}
\ No newline at end of file
+}
debian/patches/series
View file @ 694dc530
fix_classpath_in_build_xml.patch
remove_appbundler.patch
# reverted_to_antlr_4.5_deacdc96.patch
# revert_NewickLexer.java_to_antlr_4.5.patch
release/Linux/bin/applauncher
View file @ 694dc530
......@@ -27,7 +27,7 @@ BEAST_LIB="$BEAST/lib"
if [ -z "$JAVA_HOME" ]; then
JAVA=java
else
JAVA=$JAVA_HOME/bin/java
JAVA="$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 $*
"$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 $*
release/Linux/bin/beast
View file @ 694dc530
......@@ -27,16 +27,16 @@ BEAST_LIB="$BEAST/lib"
if [ -z "$JAVA_HOME" ]; then
JAVA=java
else
JAVA=$JAVA_HOME/bin/java
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:$BEAGLE_LIB
BEAST_EXTRA_LIBS="$BEAST_EXTRA_LIBS:$BEAGLE_LIB"
else
BEAST_EXTRA_LIBS=$BEAGLE_LIB
BEAST_EXTRA_LIBS="$BEAGLE_LIB"
fi
fi
......@@ -52,7 +52,7 @@ fi
# use BEAST_EXTRA_LIBS variable to load BEAGLE and other libraries from non-default locations
# this assumes that the library path contains all these libraries (or are set through LD_LIBRARY_PATH)
if [ -n "$BEAST_EXTRA_LIBS" ]; then
$JAVA -Dlauncher.wait.for.exit=true -Xms64m -Xmx4g -Djava.library.path=$BEAST_EXTRA_LIBS -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beastapp.BeastLauncher $*
"$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 $*
"$JAVA" -Dlauncher.wait.for.exit=true -Xms64m -Xmx4g -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beastapp.BeastLauncher $*
fi
release/Linux/bin/beauti
View file @ 694dc530
......@@ -27,7 +27,7 @@ BEAST_LIB="$BEAST/lib"
if [ -z "$JAVA_HOME" ]; then
JAVA=java
else
JAVA=$JAVA_HOME/bin/java
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 $*
"$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 $*
release/Linux/bin/densitree
View file @ 694dc530
......@@ -27,7 +27,7 @@ BEAST_LIB="$BEAST/lib"
if [ -z "$JAVA_HOME" ]; then
JAVA=java
else
JAVA=$JAVA_HOME/bin/java
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 $*
"$JAVA" -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/DensiTree.jar:$BEAST/DensiTree.app/Contents/Java/DensiTree.jar" viz.DensiTree $*
release/Linux/bin/loganalyser
View file @ 694dc530
......@@ -27,7 +27,7 @@ BEAST_LIB="$BEAST/lib"
if [ -z "$JAVA_HOME" ]; then
JAVA=java
else
JAVA=$JAVA_HOME/bin/java
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 $*
"$JAVA" -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/beast.jar" beast.util.LogAnalyser $*
release/Linux/bin/logcombiner
View file @ 694dc530
......@@ -27,7 +27,7 @@ BEAST_LIB="$BEAST/lib"
if [ -z "$JAVA_HOME" ]; then
JAVA=java
else
JAVA=$JAVA_HOME/bin/java
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 $*
"$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 $*
release/Linux/bin/packagemanager
View file @ 694dc530
......@@ -27,7 +27,7 @@ BEAST_LIB="$BEAST/lib"
if [ -z "$JAVA_HOME" ]; then
JAVA=java
else
JAVA=$JAVA_HOME/bin/java
JAVA="$JAVA_HOME"/bin/java
fi
$JAVA -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/beast.jar" beast.util.PackageManager $*
"$JAVA" -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/beast.jar" beast.util.PackageManager $*
release/Linux/bin/treeannotator
View file @ 694dc530
......@@ -27,7 +27,7 @@ BEAST_LIB="$BEAST/lib"
if [ -z "$JAVA_HOME" ]; then
JAVA=java
else
JAVA=$JAVA_HOME/bin/java
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.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 $*
release/Mac/launch.c 0 → 100644
View file @ 694dc530
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <mach-o/dyld.h>
void normalise(char * in, char * path) {
//char * s2 = strstr(argv[0], "BEAUti.app");
//s2[0] = 0;
//fprintf(fout, "argv0 = %s\n", in);
int i = 0 ,j = 0;
while (in[i] != 0 && i < 1024) {
char c = in[i];
if (c == ' ') {
path[j++] = '\\';
}
path[j++] = c;
i++;
}
}
int main(int argc, char *argv[]) {
char s[1024];
char buf[1024];
char path[1024];
uint32_t size = sizeof(buf);
size = _NSGetExecutablePath(buf, &size);
//FILE *fout;
//fout=fopen("/tmp/b", "w");
// fprintf(fout, "size=%lu %lu\n", strlen(buf) , strlen(argv[0]));
buf[strlen(buf) - strlen(argv[0])] = 0;
//fprintf(fout, "path = %s\n", buf);
//fprintf(fout, "argv0 = %s\n", argv[0]);
if (strstr(argv[0], "AppLauncher.app") != NULL) {
strstr(argv[0], "AppLauncher.app")[0] = 0;
normalise(argv[0], path);
sprintf(s, "%sjre1.8.0_161/bin/java -Xmx4g -Dapple.laf.useScreenMenuBar=true -Djava.library.path=$JAVAROOT:/usr/local/lib -Duser.language=en -cp %slib/launcher.jar beast.app.tools.AppLauncherLauncher", path, path);
} else if (strstr(argv[0], "BEAST.app") != NULL) {
strstr(argv[0], "BEAST.app")[0] = 0;
normalise(argv[0], path);
sprintf(s, "%sjre1.8.0_161/bin/java -Xmx4g -Dapple.laf.useScreenMenuBar=true -Djava.library.path=$JAVAROOT:/usr/local/lib -Duser.language=en -cp %slib/launcher.jar beast.app.beastapp.BeastLauncher -window -options -working", path, path);
} else if (strstr(argv[0], "DensiTree.app") != NULL) {
strstr(argv[0], "DensiTree.app")[0] = 0;
normalise(argv[0], path);
sprintf(s, "%sjre1.8.0_161/bin/java -Xmx4g -Dapple.laf.useScreenMenuBar=true -Djava.library.path=$JAVAROOT:/usr/local/lib -Duser.language=en -jar %sDensiTree.app/Contents/Java/DensiTree.jar", path, path);
} else if (strstr(argv[0], "LogCombiner.app") != NULL) {
strstr(argv[0], "LogCombiner.app")[0] = 0;
normalise(argv[0], path);
sprintf(s, "%sjre1.8.0_161/bin/java -Xmx4g -Dapple.laf.useScreenMenuBar=true -Djava.library.path=$JAVAROOT:/usr/local/lib -Duser.language=en -cp %slib/launcher.jar beast.app.tools.LogCombinerLauncher", path, path);
} else if (strstr(argv[0], "TreeAnnotator.app") != NULL) {
strstr(argv[0], "TreeAnnotator.app")[0] = 0;
normalise(argv[0], path);
sprintf(s, "%sjre1.8.0_161/bin/java -Xmx4g -Dapple.laf.useScreenMenuBar=true -Djava.library.path=$JAVAROOT:/usr/local/lib -Duser.language=en -cp %slib/launcher.jar beast.app.treeannotator.TreeAnnotatorLauncher", path, path);
} else if (strstr(argv[0], "BEAUti.app") != NULL) {
strstr(argv[0], "BEAUti.app")[0] = 0;
// fprintf(fout, "argv0 = %s\n", argv[0]);
normalise(argv[0], path);
// fprintf(fout, "path = %s\n", path);
sprintf(s, "%sjre1.8.0_161/bin/java -Xmx4g -Dapple.laf.useScreenMenuBar=true -Djava.library.path=$JAVAROOT:/usr/local/lib -Duser.language=en -cp %slib/launcher.jar beast.app.beauti.BeautiLauncher -capture", path, path);
}
//fprintf(fout,"%s\n", s);
FILE* output = popen(s, "r");
while ( fgets(buf, 1023, output) ) {
// fprintf(fout, "%s", buf);
}
pclose(output);
//fprintf(fout, "Done\n");
//fclose(fout);
return 0;
}
\ No newline at end of file
release/common/README.txt
View file @ 694dc530
BEAST v2.5.0 2018
BEAST v2.5.1 2018
Beast 2 development team 2011-2018
Last updated: April 2018
Last updated: September 2018
Contents:
1) INTRODUCTION
......