Commit 788d69cf authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.5.1+dfsg

parent 0a04b4e5

.classpath

deleted100644 → 0
+0 −14
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<?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

+3 −0
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@@ -4,5 +4,8 @@ 
/META-INF

/out



# Eclipse ignores

/.classpath



# OS X ignores

.DS_Store

Dockerfile

+2 −2
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@@ -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

+3 −2
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@@ -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

+25 −4
Original line number Diff line number Diff line
@@ -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"/>