[med-svn] [beast2-mcmc] 04/09: Readd debian/ dir with several updated regarding beast2-mcmc
Andreas Tille
tille at debian.org
Mon Sep 28 13:19:23 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository beast2-mcmc.
commit 36b6d13f5dcb4919bef9a92e19663bad12aff801
Author: Andreas Tille <tille at debian.org>
Date: Mon Sep 28 12:45:43 2015 +0200
Readd debian/ dir with several updated regarding beast2-mcmc
---
debian/README.source | 2 +
debian/README.test | 9 ++
debian/beast2-mcmc-doc.install | 2 +
debian/beast2-mcmc-examples.install | 1 +
debian/beast2-mcmc.docs | 2 +
debian/beast2-mcmc.install | 3 +
debian/beast2-mcmc.manifest | 7 +
debian/bin/beast-mcmc2 | 28 ++++
debian/bin/beauti | 5 +
debian/bin/loganalyser | 5 +
debian/bin/logcombiner | 7 +
debian/bin/treeannotator | 9 ++
debian/bin/treestat | 8 ++
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 114 +++++++++++++++++
debian/copyright | 48 +++++++
debian/libnucleotidelikelihoodcore0.install | 1 +
debian/patches/create_soname.patch | 21 +++
debian/patches/enable_hardening.patch | 21 +++
.../fix_classpath_in_build_tracer_xml.patch | 141 +++++++++++++++++++++
debian/patches/fix_classpath_in_build_xml.patch | 98 ++++++++++++++
debian/patches/fix_encoding.patch | 15 +++
debian/patches/patch_tex_docs.patch | 67 ++++++++++
debian/patches/series | 6 +
debian/rules | 75 +++++++++++
debian/source/format | 1 +
debian/tests/run-unit-test | 11 ++
debian/tracer | 11 ++
debian/upstream/metadata | 12 ++
debian/watch | 3 +
31 files changed, 739 insertions(+)
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..bf6351d
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,2 @@
+There is a new upstream release with major changes which most probably
+need a lot of packaging changes which has not yet started
diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..55102e6
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,9 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+To run the tests provided by the package you can install the package
+beast-mcmc-examples and run
+
+ sh run-unit-test
+
+in this directory.
diff --git a/debian/beast2-mcmc-doc.install b/debian/beast2-mcmc-doc.install
new file mode 100644
index 0000000..b7c85bf
--- /dev/null
+++ b/debian/beast2-mcmc-doc.install
@@ -0,0 +1,2 @@
+doc/*.pdf usr/share/doc/beast-mcmc
+doc/*/*.pdf usr/share/doc/beast-mcmc
diff --git a/debian/beast2-mcmc-examples.install b/debian/beast2-mcmc-examples.install
new file mode 100644
index 0000000..09fa917
--- /dev/null
+++ b/debian/beast2-mcmc-examples.install
@@ -0,0 +1 @@
+examples/* usr/share/doc/beast-mcmc/examples
diff --git a/debian/beast2-mcmc.docs b/debian/beast2-mcmc.docs
new file mode 100644
index 0000000..9a4f4f8
--- /dev/null
+++ b/debian/beast2-mcmc.docs
@@ -0,0 +1,2 @@
+debian/README.test
+debian/tests/run-unit-test
diff --git a/debian/beast2-mcmc.install b/debian/beast2-mcmc.install
new file mode 100644
index 0000000..d692f28
--- /dev/null
+++ b/debian/beast2-mcmc.install
@@ -0,0 +1,3 @@
+debian/bin usr
+debian/*.xpm usr/share/pixmaps
+build/dist/*.jar usr/share/beast-mcmc2
diff --git a/debian/beast2-mcmc.manifest b/debian/beast2-mcmc.manifest
new file mode 100644
index 0000000..ba5b4ca
--- /dev/null
+++ b/debian/beast2-mcmc.manifest
@@ -0,0 +1,7 @@
+/usr/share/beast-mcmc2/beast.jar:
+ Main-Class: dr.app.beast.BeastMain
+ Class-Path: /usr/share/java/beagle.jar /usr/share/java/commons-math.jar /usr/share/java/jam.jar
+
+/usr/share/beast-mcmc/beauti.jar:
+ Main-Class: dr.app.beauti.BeautiApp
+ Class-Path: /usr/share/java/beagle.jar /usr/share/java/colt.jar /usr/share/java/commons-math.jar /usr/share/java/jam.jar /usr/share/java/junit4.jar
diff --git a/debian/bin/beast-mcmc2 b/debian/bin/beast-mcmc2
new file mode 100644
index 0000000..2dea939
--- /dev/null
+++ b/debian/bin/beast-mcmc2
@@ -0,0 +1,28 @@
+#!/bin/sh
+
+# upstream has set 1024
+# I had use cases that required more than 2048
+MAXMEM=3072
+
+# Remark: There should be no need to specify CLASSPATH
+# explicitely because it is set in manifest - however, this
+# does not work
+
+# Remark: Adding /usr/lib/$(dpkg-architecture -qDEB_BUILD_MULTIARCH)/jni
+# to java.library.path helped solving the following problem:
+# $ beast-mcmc -beagle_info >/dev/null
+# Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path
+# Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path
+# Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path
+#
+# Using the setting above this turns into
+# BEAGLE resources available:
+# 0 : CPU
+# Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_SSE VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
+
+
+BEAST_LIB="/usr/share/beast-mcmc2"
+DEBJAR="/usr/share/java"
+java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="$BEAST_LIB:/usr/lib:/usr/lib/$(dpkg-architecture -qDEB_BUILD_MULTIARCH)/jni" \
+ -classpath "${CLASSPATH}:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/jdom1.jar:${DEBJAR}/colt.jar:${DEBJAR}/commons-math.jar:${DEBJAR}/treeview.jar:${BEAST_LIB}/beast.jar:$BEAST_LIB/beast-beagle.jar" \
+ dr.app.beast.BeastMain $*
diff --git a/debian/bin/beauti b/debian/bin/beauti
new file mode 100644
index 0000000..d2fe574
--- /dev/null
+++ b/debian/bin/beauti
@@ -0,0 +1,5 @@
+#!/bin/sh
+
+BEAST_LIB="/usr/share/beast-mcmc2"
+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -jar "$BEAST_LIB/beauti.jar" $*
+
diff --git a/debian/bin/loganalyser b/debian/bin/loganalyser
new file mode 100644
index 0000000..047c863
--- /dev/null
+++ b/debian/bin/loganalyser
@@ -0,0 +1,5 @@
+#!/bin/sh
+
+BEAST_LIB="/usr/share/beast-mcmc2"
+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogAnalyser $*
+
diff --git a/debian/bin/logcombiner b/debian/bin/logcombiner
new file mode 100644
index 0000000..823a270
--- /dev/null
+++ b/debian/bin/logcombiner
@@ -0,0 +1,7 @@
+#!/bin/sh
+
+BEAST_LIB="/usr/share/beast-mcmc2"
+DEBJAR="/usr/share/java"
+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
+ -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \
+ dr.app.tools.LogCombiner $*
diff --git a/debian/bin/treeannotator b/debian/bin/treeannotator
new file mode 100644
index 0000000..fd6efb3
--- /dev/null
+++ b/debian/bin/treeannotator
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+BEAST_LIB="/usr/share/beast-mcmc2"
+DEBJAR="/usr/share/java"
+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
+ -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \
+ dr.app.tools.TreeAnnotator $*
+
+
diff --git a/debian/bin/treestat b/debian/bin/treestat
new file mode 100644
index 0000000..2686a78
--- /dev/null
+++ b/debian/bin/treestat
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+BEAST_LIB="/usr/share/beast-mcmc2"
+DEBJAR="/usr/share/java"
+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
+ -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar:${DEBJAR}/jdom1.jar \
+ dr.app.treestat.TreeStatApp $*
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..f07ed49
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+beast2-mcmc (2.3.1+dfsg-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #???)
+
+ -- Andreas Tille <tille at debian.org> Mon, 28 Sep 2015 13:53:02 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..861e49a
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,114 @@
+Source: beast2-mcmc
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Olivier Sallou <osallou at debian.org>
+Section: contrib/science
+XS-Autobuild: yes
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ javahelper,
+ ant,
+ ant-optional,
+ default-jdk,
+ libjebl2-java,
+ libjam-java,
+ figtree,
+ liboptions-java,
+ libhmsbeagle-java (>= 1.1r1092),
+ libcolt-java,
+ libmpj-java,
+ r-cran-rjava,
+ libcommons-math-java (>= 2.2),
+ libjdom1-java,
+ junit4,
+ libmtj-java,
+ libitext1-java,
+ texlive-latex-base,
+ texlive-latex-extra
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/beast2-mcmc/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/beast2-mcmc/trunk/
+Homepage: http://www.beast2.org
+
+Package: beast2-mcmc
+Architecture: all
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ libhmsbeagle-java (>= 1.1r1092),
+ ${java:Depends},
+ default-jre | java6-runtime,
+ libnucleotidelikelihoodcore0 (>= ${source:Version})
+Suggests: beast-mcmc-doc
+Description: Bayesian MCMC phylogenetic inference
+ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
+ sequences. 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. Included
+ is a simple to use user-interface program for setting up standard
+ analyses and a suit of programs for analysing the results.
+ .
+ This is no new upstream version of beast-mcmc (1.x) but rather a rewritten
+ version.
+
+Package: libnucleotidelikelihoodcore0
+Architecture: amd64
+Section: contrib/libs
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Conflicts: beast-mcmc-lib
+Provides: beast-mcmc-lib
+Replaces: beast-mcmc-lib
+Description: implementation of LikelihoodCore for nucleotides used by beast-mcmc
+ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
+ sequences. 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. Included
+ is a simple to use user-interface program for setting up standard
+ analyses and a suit of programs for analysing the results.
+ .
+ This package provides an implementation of LikelihoodCore for nucleotides
+ that calls native methods for maximum speed.
+
+Package: beast2-mcmc-examples
+Architecture: all
+Section: contrib/doc
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Enhances: beast-mcmc
+Description: Bayesian MCMC phylogenetic inference - example data
+ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
+ sequences. 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. Included
+ is a simple to use user-interface program for setting up standard
+ analyses and a suit of programs for analysing the results.
+ .
+ This package contains the example data.
+
+Package: beast2-mcmc-doc
+Architecture: all
+Section: contrib/doc
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Enhances: beast-mcmc
+Description: Bayesian MCMC phylogenetic inference - documentation
+ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
+ sequences. 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. Included
+ is a simple to use user-interface program for setting up standard
+ analyses and a suit of programs for analysing the results.
+ .
+ This package contains the documentation.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..0e6cb9d
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,48 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: BEAST-MCMC
+Upstream-Contact: Alexei Drummond <alexei at cs.auckland.ac.nz>,
+ Andrew Rambaut <a.rambaut at ed.ac.uk>
+Source: http://beast-mcmc.googlecode.com/svn/trunk/
+Files-Excluded: *.jar
+ *.so
+ *.o
+ *.jnilib
+
+Files: *
+Copyright: 2002-2011 Alexei Drummond and Andrew Rambaut
+License: LGPL-3+
+
+Files: src/dr/math/matrixAlgebra/RobustSingularValueDecomposition.java
+Copyright: 1999 CERN - European Organization for Nuclear Research
+ 1999 Marc A. Suchard
+License: Colt-License-Agreement
+ Permission to use, copy, modify, distribute and sell this software and its
+ documentation for any purpose is hereby granted without fee, provided that
+ the above copyright notice appear in all copies and that both that
+ copyright notice and this permission notice appear in supporting
+ documentation. CERN makes no representations about the suitability of this
+ software for any purpose. It is provided "as is" without expressed or
+ implied warranty.
+
+Files: debian/*
+Copyright: 2011-2012 Andreas Tille <tille at debian.org>
+License: LGPL-3+
+
+License: LGPL-3+
+ This program 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 3 of the License, or
+ (at your option) any later version.
+ .
+ This program 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 General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On a Debian GNU/Linux system, the GNU Lesser GPL license version 3 is included
+ in the file ‘/usr/share/common-licenses/LGPL-3’, and the GNU GPL license
+ version 3 is included in the file ‘/usr/share/common-licenses/GPL-3’.
+
diff --git a/debian/libnucleotidelikelihoodcore0.install b/debian/libnucleotidelikelihoodcore0.install
new file mode 100644
index 0000000..36715b0
--- /dev/null
+++ b/debian/libnucleotidelikelihoodcore0.install
@@ -0,0 +1 @@
+native/l*.so* usr/lib
diff --git a/debian/patches/create_soname.patch b/debian/patches/create_soname.patch
new file mode 100644
index 0000000..50e3bf2
--- /dev/null
+++ b/debian/patches/create_soname.patch
@@ -0,0 +1,21 @@
+Description: Create SONAME for library
+Author: Andreas Tille <tille at debian.org>
+Created: Mon, 17 Dec 2012 16:43:17 +0100
+
+--- beast-mcmc-1.8.0.orig/native/Makefile.linux
++++ beast-mcmc-1.8.0/native/Makefile.linux
+@@ -1,11 +1,11 @@
+ CC=gcc
+-CFLAGS += -O2 -funroll-loops
++CFLAGS=-O2 -funroll-loops
+ INCLUDES=-I${JAVA_HOME}/include/ -I${JAVA_HOME}/include/linux
+
+ OBJS = NucleotideLikelihoodCore.o
+
+ .c.o:
+- ${CC} $(CPPFLAGS) ${CFLAGS} $(LDFLAGS) ${INCLUDES} -c $*.c
++ ${CC} ${CFLAGS} ${INCLUDES} -c $*.c
+
+ libNucleotideLikelihoodCore.so: ${OBJS}
+- ${CC} $(CPPFLAGS) ${CFLAGS} $(LDFLAGS) ${INCLUDES} -shared -o libNucleotideLikelihoodCore.so ${OBJS}
++ ${CC} ${CFLAGS} ${INCLUDES} -shared -Wl,-soname,libNucleotideLikelihoodCore.so.0 -o libNucleotideLikelihoodCore.so.0 ${OBJS}
diff --git a/debian/patches/enable_hardening.patch b/debian/patches/enable_hardening.patch
new file mode 100644
index 0000000..0df658f
--- /dev/null
+++ b/debian/patches/enable_hardening.patch
@@ -0,0 +1,21 @@
+Description: Enable propagation of hardening flags
+Author: Andreas Tille <tille at debian.org>
+Date: Tue, 05 Jun 2012 14:38:11 +0200
+
+--- beast-mcmc-1.8.0.orig/native/Makefile.linux
++++ beast-mcmc-1.8.0/native/Makefile.linux
+@@ -1,11 +1,11 @@
+ CC=gcc
+-CFLAGS=-O2 -funroll-loops
++CFLAGS += -O2 -funroll-loops
+ INCLUDES=-I${JAVA_HOME}/include/ -I${JAVA_HOME}/include/linux
+
+ OBJS = NucleotideLikelihoodCore.o
+
+ .c.o:
+- ${CC} ${CFLAGS} ${INCLUDES} -c $*.c
++ ${CC} $(CPPFLAGS) ${CFLAGS} $(LDFLAGS) ${INCLUDES} -c $*.c
+
+ libNucleotideLikelihoodCore.so: ${OBJS}
+- ${CC} ${CFLAGS} ${INCLUDES} -shared -o libNucleotideLikelihoodCore.so ${OBJS}
++ ${CC} $(CPPFLAGS) ${CFLAGS} $(LDFLAGS) ${INCLUDES} -shared -o libNucleotideLikelihoodCore.so ${OBJS}
diff --git a/debian/patches/fix_classpath_in_build_tracer_xml.patch b/debian/patches/fix_classpath_in_build_tracer_xml.patch
new file mode 100644
index 0000000..5715a02
--- /dev/null
+++ b/debian/patches/fix_classpath_in_build_tracer_xml.patch
@@ -0,0 +1,141 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Tue, 10 Jan 2012 22:29:24 +0100
+Description: Make sure also tracer is builded with Debian packages JARs
+
+--- beast-mcmc-1.8.0.orig/build_tracer.xml
++++ beast-mcmc-1.8.0/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 ${build} -->
+ <javac source="1.5" target="1.5" srcdir="${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:${deblib}/mtj.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar:${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-2.0.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>
+@@ -136,46 +137,12 @@
+
+ <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="${Linux_package_dir}" />
+@@ -200,55 +167,4 @@
+ <echo message="Linux/Unix version release is finished." />
+ </target>
+
+- <target name="mac"
+- description="release Mac version of Tracer">
+- <delete dir="${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"
+- icon="${Mac_dir}/icons/Tracer.icns"
+- jvmversion="1.5+"
+- vmoptions="-Xmx1024M"
+- arguments=""
+- version="${version}"
+- infostring="${name} v${version}, Copyright 2003-2009, Andrew Rambaut & 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${version}.dmg"/>
+- </exec>
+-
+- <echo message="Mac version release is finished." />
+- </target>
+-
+ </project>
diff --git a/debian/patches/fix_classpath_in_build_xml.patch b/debian/patches/fix_classpath_in_build_xml.patch
new file mode 100644
index 0000000..e6ae98e
--- /dev/null
+++ b/debian/patches/fix_classpath_in_build_xml.patch
@@ -0,0 +1,98 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Updated: 2012-02-26
+Subject: use Debian jars
+Description: Make sure package builds with Debian packages JARs
+Forwarded: no
+--- beast-mcmc-1.8.0.orig/build.xml
++++ beast-mcmc-1.8.0/build.xml
+@@ -36,6 +36,7 @@
+ <property name="src" location="src"/>
+ <property name="build" location="build"/>
+ <property name="lib" location="lib"/>
++ <property name="deblib" location="/usr/share/java" />
+ <property name="dist" location="${build}/dist"/>
+
+ <property name="main_class_BEAST" value="dr.app.beast.BeastMain"/>
+@@ -47,6 +48,19 @@
+
+ <path id="classpath">
+ <fileset dir="${lib}" includes="**/*.jar"/>
++ <fileset dir="${deblib}" includes="beagle.jar"/>
++ <fileset dir="${deblib}" includes="colt.jar"/>
++ <fileset dir="${deblib}" includes="commons-math.jar"/>
++ <fileset dir="${deblib}" includes="figtree.jar"/>
++ <fileset dir="${deblib}" includes="itext1.jar"/>
++ <fileset dir="${deblib}" includes="jam.jar"/>
++ <fileset dir="${deblib}" includes="jdom1.jar"/>
++ <fileset dir="${deblib}" includes="jebl.jar"/>
++ <fileset dir="/usr/lib/R/site-library/rJava/jri/" includes="JRI.jar"/>
++ <fileset dir="${deblib}" includes="junit4.jar"/>
++ <fileset dir="${deblib}" includes="mpj.jar"/>
++ <fileset dir="${deblib}" includes="mtj.jar"/>
++ <fileset dir="${deblib}" includes="options.jar"/>
+ </path>
+
+ <!-- start -->
+@@ -159,14 +173,6 @@
+ <include name="org/virion/jam/**/*.png"/>
+ <include name="dr/**/*.properties"/>
+ </fileset>
+- <zipgroupfileset dir="${lib}" includes="jebl.jar"/>
+- <zipgroupfileset dir="${lib}" includes="jam.jar"/>
+- <zipgroupfileset dir="${lib}" includes="jdom.jar"/>
+- <zipgroupfileset dir="${lib}" includes="commons-math-2.2.jar"/>
+- <zipgroupfileset dir="${lib}" includes="mtj.jar"/>
+- <zipgroupfileset dir="${lib}" includes="JRI.jar"/>
+- <zipgroupfileset dir="${lib}" includes="colt.jar"/>
+- <zipgroupfileset dir="${lib}" includes="beagle.jar"/>
+ </jar>
+
+ <!-- Put everything in ${build} into the beauti.jar file -->
+@@ -222,11 +228,6 @@
+ <fileset dir="${src}">
+ <include name="dr/**/*.png"/>
+ </fileset>
+- <zipgroupfileset dir="${lib}" includes="jam.jar"/>
+- <zipgroupfileset dir="${lib}" includes="jebl.jar"/>
+- <zipgroupfileset dir="${lib}" includes="jdom.jar"/>
+- <zipgroupfileset dir="${lib}" includes="commons-math-2.2.jar"/>
+- <zipgroupfileset dir="${lib}" includes="mtj.jar"/>
+ </jar>
+
+ </target>
+--- beast-mcmc-1.8.0.orig/.classpath
++++ beast-mcmc-1.8.0/.classpath
+@@ -1,20 +1,20 @@
+ <?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/figtreepanel.jar"/>
+- <classpathentry kind="lib" path="lib/itext-1.4.5.jar"/>
+- <classpathentry kind="lib" path="lib/jam.jar"/>
+- <classpathentry kind="lib" path="lib/jdom.jar"/>
+- <classpathentry kind="lib" path="lib/jebl.jar"/>
+- <classpathentry kind="lib" path="lib/JRI.jar"/>
+- <classpathentry kind="lib" path="lib/junit-4.4.jar"/>
+- <classpathentry kind="lib" path="lib/mpj.jar"/>
+- <classpathentry kind="lib" path="lib/mtj.jar"/>
+- <classpathentry kind="lib" path="lib/options.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/beagle.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/colt.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/figtreepanel.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/itext-1.4.5.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/jam.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/jdom.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/jebl.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/JRI.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/junit-4.4.jar"/>
++ <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/options.jar"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+- <classpathentry kind="lib" path="lib/commons-math-2.2.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/commons-math-2.2.jar"/>
+ <classpathentry kind="output" path="bin"/>
+ </classpath>
+
diff --git a/debian/patches/fix_encoding.patch b/debian/patches/fix_encoding.patch
new file mode 100644
index 0000000..3182443
--- /dev/null
+++ b/debian/patches/fix_encoding.patch
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 30 Sep 2014 18:15:36 +0200
+Description: Fix encoding issue
+
+--- beast-mcmc-1.8.0.orig/src/dr/app/beauti/siteModelsPanel/PartitionModelPanel.java
++++ beast-mcmc-1.8.0/src/dr/app/beauti/siteModelsPanel/PartitionModelPanel.java
+@@ -243,7 +243,7 @@
+ PanelUtils.setupComponent(setYang96Button);
+ setYang96Button
+ .setToolTipText("<html>Sets a 3 codon-position model with independent GTR and Gamma as described in<br>"
+- + "Yang (1996) <i>J Mol Evol</i> <b>42</b>: 587–596. This model is named 3' in this paper.</html>");
++ + "Yang (1996) <i>J Mol Evol</i> <b>42</b>: 587-596. This model is named 3' in this paper.</html>");
+
+ setSRD06Button = new JButton("Use SRD06 model");
+ setSRD06Button.addActionListener(new ActionListener() {
diff --git a/debian/patches/patch_tex_docs.patch b/debian/patches/patch_tex_docs.patch
new file mode 100644
index 0000000..ee5b738
--- /dev/null
+++ b/debian/patches/patch_tex_docs.patch
@@ -0,0 +1,67 @@
+Description: Fix some latex error that are preventing proper creation of docs
+Author: Andreas Tille <tille at debian.org>
+Date: Tue, 05 Jun 2012 14:38:11 +0200
+LastUpdated: Mon, 17 Dec 2012 16:43:17 +0100
+
+--- beast-mcmc-1.8.0.orig/doc/Yule.tex
++++ beast-mcmc-1.8.0/doc/Yule.tex
+@@ -35,6 +35,7 @@
+ \begin{document}
+
+ \title{\textbf{The Yule model}}
++\date{22. May, 2007}
+
+ \author{\textsc{Alexei J. Drummond}}
+
+--- beast-mcmc-1.8.0.orig/doc/BookSection/BookSection.tex
++++ beast-mcmc-1.8.0/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}
+--- beast-mcmc-1.8.0.orig/doc/SerialSampleCoalescent.tex
++++ beast-mcmc-1.8.0/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
+--- beast-mcmc-1.8.0.orig/doc/BEAST14_Manual.tex
++++ beast-mcmc-1.8.0/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}$\\
+--- beast-mcmc-1.8.0.orig/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex
++++ beast-mcmc-1.8.0/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex
+@@ -789,7 +789,7 @@
+
+ \medskip{}
+
+-\includegraphics[scale=0.4]{figures3/BEAUti_Prior}
++\includegraphics[scale=0.4]{figures3/BEAUTi_Prior}
+
+ \medskip{}
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..c01f0dd
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,6 @@
+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
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..d073e6e
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,75 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# debian/rules file for beast-mcmc
+# Andreas Tille <tille at debian.org>
+# GPL
+
+#export DH_VERBOSE=1
+
+PACKAGE := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
+
+JAVA_HOME := /usr/lib/jvm/default-java
+
+DEBJAR := /usr/share/java
+CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:$(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
+
+# to run the test suite
+JAVA := $(JAVA_HOME)/bin/java
+ANT_HOME := /usr/share/ant
+ANT_BIN := $(ANT_HOME)/bin/ant
+ANT_ARGS := -Dcompile.debug=true -Dcompile.optimize=true
+
+%:
+ dh $@ --with javahelper
+
+override_dh_auto_clean:
+ rm -f native/*\.o native/*\.so native/*\.so\.*
+ for cleantex in \
+ Practical_BEAST \
+ BookSection \
+ Practical_BEAST \
+ Yule \
+ SerialSampleCoalescent \
+ BEAST14_Manual \
+ ; do \
+ find doc -not -name "*.tex" -a -not -name "*.bib" -and -name "$${cleantex}.*" -exec rm -f \{\} \; ; \
+ done
+ ant clean
+
+CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
+PDFLATEX:=pdflatex -interaction=batchmode
+
+override_dh_auto_build:
+ # CLASSPATH=$(CLASS_PATH)
+ ant build
+ ant -buildfile build_tracer.xml all
+ # native/compileNativeLinux.sh does not create dynamic libraries
+ cd native ; $(MAKE) -f Makefile.linux JAVA_HOME=$(JAVA_HOME)
+# gcc $(CFLAGS) $(LDFLAGS) -Wall -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ NucleotideLikelihoodCore.c -o libNucleotideLikelihoodCore.o ; \
+# 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
+ #
+ # Build extra LaTeX documentation
+ #
+ cd doc/BookSection; $(PDFLATEX) BookSection.tex; $(PDFLATEX) BookSection.tex
+ cd doc/tutorial/Virus_Practical*; $(PDFLATEX) Practical_BEAST.tex; $(PDFLATEX) Practical_BEAST.tex
+ 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
+ #
+ #####################################################################
+ ## Run test suite ##
+ ## -------------- ##
+ ## While this test suite runs quite a bit of time (about 30min) it ##
+ ## is recommended to be run at least once per new version upload ##
+ #####################################################################
+ #
+ # $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml junit
+
+override_dh_compress:
+ dh_compress --exclude=.pdf
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compression xz
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100755
index 0000000..5d10958
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,11 @@
+#!/bin/bash -e
+pkg=beast-mcmc
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+
+for file in /usr/share/doc/beast-mcmc/examples/*/*\.xml
+do
+ beast-mcmc -overwrite $file
+done
\ No newline at end of file
diff --git a/debian/tracer b/debian/tracer
new file mode 100644
index 0000000..32afa6e
--- /dev/null
+++ b/debian/tracer
@@ -0,0 +1,11 @@
+#!/bin/sh
+
+echo "dr/app/tracer/application/TracerApp is missing in beast.jar - build system needs fixing!"
+exit 1
+
+BEAST_LIB="/usr/share/beast-mcmc"
+DEBJAR="/usr/share/java"
+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
+ -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \
+ dr/app/tracer/application/TracerApp $*
+
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..9ce71b4
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Alexei J Drummond and Andrew Rambaut
+ Title: "BEAST: Bayesian evolutionary analysis by sampling trees"
+ Journal: BMC Evol Biol
+ Year: 2007
+ Volume: 8
+ Number: 7
+ Pages: 214
+ DOI: 10.1186/1471-2148-7-214
+ PMID: 17996036
+ URL: http://www.biomedcentral.com/1471-2148/7/214/abstract
+ eprint: http://www.biomedcentral.com/content/pdf/1471-2148-7-214.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..e6dbdc2
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+ https://github.com/CompEvol/beast2/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/beast2-mcmc.git
More information about the debian-med-commit
mailing list