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build.xml
View file @ ca64e229
......@@ -256,8 +256,8 @@
<!-- Release -->
<property name="version" value="2.5.1" />
<property name="version_number" value="2.5.1" />
<property name="version" value="2.5.2" />
<property name="version_number" value="2.5.2" />
<property name="release_dir" value="release" />
<property name="copyright" value="Beast 2 development team 2011-2018" />
......@@ -550,6 +550,139 @@
<echo message="Windows version release is finished." />
</target>
<target name="windowsjre2"
description="release Windows version of BEAST, BEAUTI, TreeAnnotator, LogCombiner">
<delete dir="${Windows_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Windows_package_dir}" />
<property name="launch4j.dir" location="../launch4j" />
<taskdef name="launch4j"
classname="net.sf.launch4j.ant.Launch4jTask"
classpath="${launch4j.dir}/launch4j.jar :${launch4j.dir}/lib/xstream.jar" />
<copy todir="${Windows_package_dir}/examples/">
<fileset dir="examples/">
<include name="*.xml" />
<include name="nexus/**" />
<exclude name="benchmark/**" />
</fileset>
</copy>
<copy todir="${Windows_package_dir}/jre">
<fileset dir="../jre1.8.0_161" />
</copy>
<!--<copy todir="${Windows_package_dir}/native">
<fileset dir="${common_dir}/native"/>
</copy>
<copy todir="${Windows_package_dir}/doc">
<fileset dir="${common_dir}/doc" />
</copy>
<copy todir="${Windows_package_dir}/bin">
<fileset dir="${Windows_dir}/scripts"/>
</copy>
<copy file="${dist}/beauti.jar" todir="${Windows_package_dir}/lib"/>-->
<copy file="${dist}/beast.jar" todir="${Windows_package_dir}/lib" />
<copy file="${dist}/beast.src.jar" todir="${Windows_package_dir}/lib" />
<!-- <copy file="${dist}/beast-beagle.jar" todir="${Windows_package_dir}/lib"/>
<copy todir="${Windows_package_dir}/lib">
<fileset dir="${Windows_dir}/lib"/>
</copy>-->
<copy file="${common_dir}/VERSION HISTORY.txt" todir="${Windows_package_dir}" />
<copy file="${common_dir}/README.txt" todir="${Windows_package_dir}" />
<copy file="${common_dir}/LICENSE.txt" todir="${Windows_package_dir}" />
<!-- BEAUTi v?.?.?.exe -->
<launch4j configFile="${Windows_dir}/BEAUti_launch4j_jre2.xml"
jar="${dist}/beast.jar"
outfile="${Windows_package_dir}/${BEAUti_name}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}" >
<!-- to bunle a JRE, copy the desired JRE to folder ../jre
(so java.exe is in ../jre/bin/) and uncomment following fragment
TODO: needs testing
<jre>
<path>../jre</path>
</jre>
-->
</launch4j>
<!-- BEAST v?.?.?.exe -->
<launch4j configFile="${Windows_dir}/BEAST_launch4j_jre2.xml"
jar="${dist}/beast.jar"
outfile="${Windows_package_dir}/${BEAST_name}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}" />
<!--<launch4j configFile="${Windows_dir}/TreeStat_launch4j.xml"
jar="${dist}/beast.jar"
outfile="${Windows_package_dir}/${TreeStat_name}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}"/>-->
<!-- LogAnalyser v?.?.?.exe
<launch4j configFile="${Windows_dir}/LogAnalyser_launch4j_jre.xml"
jar="${dist}/beast.jar"
outfile="${Windows_package_dir}/${LogAnalyser_name}v${version}.exe"
fileVersion="${version}.0"
txtFileVersion="${version}"
productVersion="${version}.0"
txtProductVersion="${version}"/> -->
<launch4j configFile="${Windows_dir}/LogCombiner_launch4j_jre2.xml"
jar="${dist}/beast.jar"
outfile="${Windows_package_dir}/${LogCombiner_name}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}"/>
<launch4j configFile="${Windows_dir}/TreeAnnotator_launch4j_jre2.xml"
jar="${dist}/beast.jar"
outfile="${Windows_package_dir}/TreeAnnotator.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}"/>
<launch4j configFile="${tools_dir}/DensiTree_launch4j_jre.xml"
jar="${tools_dir}/DensiTree.jar"
outfile="${Windows_package_dir}/DensiTree.exe"
fileVersion="2.0.0.0"
txtFileVersion="2.0.0.0"
productVersion="2.0.0.0"
txtProductVersion="2.0.0.0" />
<launch4j configFile="${Windows_dir}/AppLauncher_launch4j_jre2.xml"
jar="${dist}/beast.jar"
outfile="${Windows_package_dir}/AppLauncher.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}"/>
<copy todir="${Windows_package_dir}/templates/">
<fileset dir="templates/" />
</copy>
<!--
<copy file="${beast1_dir}/LogCombiner.exe" todir="${Windows_package_dir}" />
<copy file="${beast1_dir}/TreeAnnotator.exe" todir="${Windows_package_dir}" />
-->
<zip destfile="${Windows_dir}/${BEAST_name}.v${version}.zip">
<zipfileset dir="${Windows_package_dir}" prefix="${BEAST_name}" />
</zip>
<copy file="${Windows_dir}/${BEAST_name}.v${version}.zip" todir="../../tmp/" />
<echo message="Windows version release is finished." />
</target>
<target name="linux"
depends="build_jar_all_BEAST_NoJUnitTest"
description="release Linux/Unix version of BEAST, BEAUTI, TreeAnnotator, LogCombiner">
......
debian/changelog
View file @ ca64e229
beast2-mcmc (2.5.2+dfsg-1) UNRELEASED; urgency=medium
* New upstream release
-- Olivier Sallou <osallou@debian.org> Sun, 10 Mar 2019 16:23:06 +0000
beast2-mcmc (2.5.1+dfsg-2) unstable; urgency=medium
* Avoid Mac only code which is not needed and fails due missing
......
debian/patches/antlr-compatibility.patch
View file @ ca64e229
......@@ -3,7 +3,7 @@ Author: Emmanuel Bourg <ebourg@apache.org>
Forwarded: not-needed
--- a/src/beast/util/TreeParser.java
+++ b/src/beast/util/TreeParser.java
@@ -349,8 +349,6 @@
@@ -374,8 +374,6 @@
* @return root node of tree
*/
public Node parseNewick(String newick) {
......@@ -12,7 +12,7 @@ Forwarded: not-needed
// Custom parse/lexer error listener
BaseErrorListener errorListener = new BaseErrorListener() {
@Override
@@ -364,7 +362,7 @@
@@ -389,7 +387,7 @@
// Use lexer to produce token stream
......
debian/patches/remove_appbundler.patch
View file @ ca64e229
......@@ -5,7 +5,7 @@ Description: Remove mac specific stuff breaking build on Linux when not
--- a/build.xml
+++ b/build.xml
@@ -689,9 +689,6 @@
@@ -822,9 +822,6 @@
<echo message="cp BEAST.v${version}.tgz ~/tmp"/>
</target>
......
debian/patches/remove_mac_only_code.patch
View file @ ca64e229
......@@ -6,7 +6,7 @@ Last-Update: Sat, 26 Jan 2019 08:08:17 +0100
--- a/src/beast/app/beauti/Beauti.java
+++ b/src/beast/app/beauti/Beauti.java
@@ -1231,6 +1231,7 @@ public class Beauti extends JTabbedPane
@@ -1235,6 +1235,7 @@
if (Utils.isMac() && Utils6.isMajorAtLeast(Utils6.JAVA_1_8)) {
// set up application about-menu for Mac
// Mac-only stuff
......@@ -14,7 +14,7 @@ Last-Update: Sat, 26 Jan 2019 08:08:17 +0100
try {
URL url = ClassLoader.getSystemResource(ModelBuilder.ICONPATH + "beauti.png");
Icon icon = null;
@@ -1268,10 +1269,7 @@ public class Beauti extends JTabbedPane
@@ -1272,10 +1273,7 @@
};
// https://github.com/CompEvol/beast2/issues/805
......@@ -25,7 +25,7 @@ Last-Update: Sat, 26 Jan 2019 08:08:17 +0100
} catch (Exception e) {
// ignore
}
@@ -1284,6 +1282,7 @@ public class Beauti extends JTabbedPane
@@ -1288,6 +1286,7 @@
// ignore
}
}
......
debian/rules
View file @ ca64e229
......@@ -34,3 +34,6 @@ override_dh_auto_build:
override_dh_compress:
dh_compress --exclude=.pdf
override_dh_auto_clean:
# skip as it needs patches applied
doc/tutorials/DivergenceDating/DivergenceDatingTutorial.bib
View file @ ca64e229
......@@ -108,4 +108,4 @@
Title = {Calibrated tree priors for relaxed phylogenetics and divergence time estimation},
Volume = {61},
Year = {2012},
Bdsk-Url-1 = {http://dx.doi.org/10.1093/sysbio/syr087}}
Bdsk-Url-1 = {https://doi.org/10.1093/sysbio/syr087}}
doc/tutorials/EBSP/ebsp2-tut.bib
View file @ ca64e229
......@@ -23,7 +23,7 @@
Pii = {PCOMPBIOL-D-13-02115},
Pmid = {24722319},
Timestamp = {2015.05.07},
Url = {http://dx.doi.org/10.1371/journal.pcbi.1003537}
Url = {https://doi.org/10.1371/journal.pcbi.1003537}
}
@Article{Heled2008,
......@@ -46,6 +46,6 @@
Pii = {1471-2148-8-289},
Pmid = {18947398},
Timestamp = {2016.01.11},
Url = {http://dx.doi.org/10.1186/1471-2148-8-289}
Url = {https://doi.org/10.1186/1471-2148-8-289}
}
doc/tutorials/MEPs/MEPs.bib
View file @ ca64e229
......@@ -34,5 +34,5 @@
Title = {Genetic variability and molecular evolution of the human respiratory syncytial virus subgroup B attachment G protein},
Volume = {79},
Year = {2005},
Bdsk-Url-1 = {http://dx.doi.org/10.1128/JVI.79.14.9157-9167.2005}}
Bdsk-Url-1 = {https://doi.org/10.1128/JVI.79.14.9157-9167.2005}}
doc/tutorials/STACEY/STACEY_tutorial.bib
View file @ ca64e229
......@@ -16,7 +16,7 @@
Title = {Bayesian inference of species trees from multilocus data},
Volume = {27},
Year = {2010},
Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/msp274}}
Bdsk-Url-1 = {https://doi.org/10.1093/molbev/msp274}}
@inproceedings{hohna2008clock,
......
doc/tutorials/STARBEAST/StarBEAST_tutorial.bib
View file @ ca64e229
......@@ -16,7 +16,7 @@
Title = {Bayesian inference of species trees from multilocus data},
Volume = {27},
Year = {2010},
Bdsk-Url-1 = {http://dx.doi.org/10.1093/molbev/msp274}}
Bdsk-Url-1 = {https://doi.org/10.1093/molbev/msp274}}
@article{belfiore2008multilocus,
......@@ -49,4 +49,4 @@ and Vaughan, Tim and Wu, Chieh-Hsi and Xie, Dong and Suchard, Marc A and Rambaut
Title = {BEAST 2: a software platform for Bayesian evolutionary analysis},
Volume = {10},
Year = {2014},
Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pcbi.1003537}}
Bdsk-Url-1 = {https://doi.org/10.1371/journal.pcbi.1003537}}
examples/nexus/humanChimpSNP.nex
View file @ ca64e229
......@@ -10,10 +10,12 @@ Yoruba 00000000000000000000000000111111111111111111111111111222222222222222
European 0000000011111111122222222200000000011111111122222222200000000011111111122222222200000000011111111122222222200000000011111111122222222200000000011111111122222222200000000011111111122222222200000000011111111122222222200000000011111111122222222200000000011111111122222222200000000011111111122222222200000000011111111122222222200000000011111111122222222200000000011111111122222222200000000011111111122222222200000000011111111122222222200000000011111111122222222200000000011111111122222222
Han 0011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122200011122
Korean 1201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201
;
End;
begin assumptions;
wtset MyWeights (VECTOR) = 1517 141 1526 487 159 151 161 84 2340 357 74 331 307 155 85 127 116 227 96 40 98 114 88 33 66 157 3896 202 39 253 178 59 34 66 43 394 143 41 149 154 91 44 74 118 88 47 20 65 91 70 29 65 202 284 44 14 27 40 17 5 20 23 72 27 5 32 35 25 6 34 58 28 14 11 14 32 36 8 31 201 5058 141 34 166 141 39 34 41 50 249 88 27 87 81 46 14 33 59 77 29 9 42 45 40 23 35 111 639 97 16 90 101 45 24 33 45 132 56 26 72 119 73 23 61 100 50 35 12 43 71 68 18 79 300 133 28 9 25 37 20 3 19 27 62 29 9 36 41 39 13 42 92 23 23 15 18 53 64 18 53 607 679 39 8 31 36 17 9 13 19 58 23 8 32 31 20 12 15 45 19 13 4 9 21 21 7 24 72 196 44 11 39 44 23 18 21 28 61 28 11 39 48 58 11 36 97 23 23 17 18 33 69 11 66 475 63 21 5 25 28 20 15 17 32 34 24 16 27 47 43 14 40 171 17 24 19 23 69 127 25 102 147388 144522 126 24 135 70 21 15 23 22 169 39 6 59 48 28 21 27 32 37 18 9 22 27 19 9 26 81 450 64 17 63 59 21 12 31 24 112 38 16 58 68 37 28 38 73 25 35 9 20 37 42 9 48 229 90 28 5 21 26 6 6 12 16 42 16 10 32 35 41 4 34 70 14 10 19 9 37 55 7 52 701 670 73 27 72 56 26 17 26 28 97 37 16 36 65 36 16 48 57 33 19 7 28 37 36 7 49 154 321 80 18 79 80 39 21 46 50 107 62 30 83 129 72 32 99 179 47 43 23 56 73 104 22 125 810 121 47 21 47 71 52 13 33 73 83 52 25 63 89 116 35 104 281 36 67 36 53 152 200 45 171 6270 238 43 5 29 39 23 13 9 26 68 27 9 42 65 44 12 37 62 20 29 13 23 33 50 11 72 385 231 72 47 85 108 61 23 69 101 110 89 48 92 166 185 54 168 475 78 79 53 102 199 272 56 269 4863 173 90 36 94 172 112 54 131 336 145 158 107 176 376 447 103 445 2773 139 183 207 226 665 1906 218 1953
;
end;
release/Linux/jrebin/applauncher
View file @ ca64e229
......@@ -28,7 +28,7 @@ BEAST_LIB="$BEAST/lib"
if [ -z "$JAVA_HOME" ]; then
JAVA=java
else
JAVA=$JAVA_HOME/bin/java
JAVA="$JAVA_HOME"/bin/java
fi
$JAVA -Dlauncher.wait.for.exit=true -Dlauncher.wait.for.exit=true -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.tools.AppLauncherLauncher $*
"$JAVA" -Dlauncher.wait.for.exit=true -Dlauncher.wait.for.exit=true -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.tools.AppLauncherLauncher $*
release/Linux/jrebin/beast
View file @ ca64e229
......@@ -28,16 +28,16 @@ BEAST_LIB="$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="$BEAGLE_LIB"
fi
fi
......@@ -53,7 +53,7 @@ fi
# use BEAST_EXTRA_LIBS variable to load BEAGLE and other libraries from non-default locations
# this assumes that the library path contains all these libraries (or are set through LD_LIBRARY_PATH)
if [ -n "$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 $*
fi
release/Linux/jrebin/beauti
View file @ ca64e229
......@@ -28,7 +28,7 @@ BEAST_LIB="$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 $*
release/Linux/jrebin/densitree
View file @ ca64e229
......@@ -28,7 +28,7 @@ BEAST_LIB="$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 $*
release/Linux/jrebin/loganalyser
View file @ ca64e229
......@@ -28,7 +28,7 @@ BEAST_LIB="$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 $*
release/Linux/jrebin/logcombiner
View file @ ca64e229
......@@ -28,7 +28,7 @@ BEAST_LIB="$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 $*
release/Linux/jrebin/packagemanager
View file @ ca64e229
......@@ -28,7 +28,7 @@ BEAST_LIB="$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 $*
release/Linux/jrebin/treeannotator
View file @ ca64e229
......@@ -28,7 +28,7 @@ BEAST_LIB="$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 $*