New upstream version 2.5.2+dfsg (5d49e7d8) · Commits · Debian Med / beast2-mcmc

build.xml

+135 −2

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		@@ -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">

doc/tutorials/DivergenceDating/DivergenceDatingTutorial.bib

+1 −1

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		@@ -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

+2 −2

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		@@ -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

+1 −1

Original line number	Diff line number	Diff line
		@@ -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

+1 −1

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		@@ -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,