[med-svn] r5696 - in trunk/packages/beast-mcmc/trunk/debian: . patches
Felix Feyertag
fxf-guest at alioth.debian.org
Mon Jan 24 16:50:26 UTC 2011
Author: fxf-guest
Date: 2011-01-24 16:50:26 +0000 (Mon, 24 Jan 2011)
New Revision: 5696
Modified:
trunk/packages/beast-mcmc/trunk/debian/changelog
trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch
trunk/packages/beast-mcmc/trunk/debian/patches/series
trunk/packages/beast-mcmc/trunk/debian/rules
Log:
* New upstream release
Modified: trunk/packages/beast-mcmc/trunk/debian/changelog
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/changelog 2011-01-24 15:31:09 UTC (rev 5695)
+++ trunk/packages/beast-mcmc/trunk/debian/changelog 2011-01-24 16:50:26 UTC (rev 5696)
@@ -1,3 +1,9 @@
+beast-mcmc (1.6.1+svnr3660-1) UNRELEASED; urgency=low
+
+ * New upstream release
+
+ -- Felix Feyertag <fx at atalanta> Mon, 24 Jan 2011 14:17:58 +0100
+
beast-mcmc (1.5.4+svnr3087-1) UNRELEASED; urgency=low
* New upstream release
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch 2011-01-24 15:31:09 UTC (rev 5695)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch 2011-01-24 16:50:26 UTC (rev 5696)
@@ -1,9 +1,198 @@
---- beast-mcmc-1.5.3+svnr2672.orig/scripts/beast
-+++ beast-mcmc-1.5.3+svnr2672/scripts/beast
-@@ -23,5 +23,5 @@
- fi
+Index: beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/beast
+===================================================================
+--- beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/beast 2011-01-24 16:39:22.000000000 +0000
++++ beast-mcmc-1.6.1+svnr3660/release/Linux/scripts/beast 2011-01-24 16:39:41.000000000 +0000
+@@ -1,26 +1,4 @@
+ #!/bin/sh
- BEAST_LIB=$BEAST/lib
--java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -jar $BEAST_LIB/beast.jar $*
+-if [ -z "$BEAST" ]; then
+- ## resolve links - $0 may be a link to application
+- PRG="$0"
+-
+- # need this for relative symlinks
+- while [ -h "$PRG" ] ; do
+- ls=`ls -ld "$PRG"`
+- link=`expr "$ls" : '.*-> \(.*\)$'`
+- if expr "$link" : '/.*' > /dev/null; then
+- PRG="$link"
+- else
+- PRG="`dirname "$PRG"`/$link"
+- fi
+- done
+-
+- # make it fully qualified
+- saveddir=`pwd`
+- BEAST0=`dirname "$PRG"`/..
+- BEAST=`cd "$BEAST0" && pwd`
+- cd "$saveddir"
+-fi
+-
+-BEAST_LIB="$BEAST/lib"
+-java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB:/usr/local/lib" -cp "$BEAST_LIB/beast.jar:$BEAST_LIB/beast-beagle.jar" dr.app.beast.BeastMain $*
++BEAST_LIB="/usr/share/beast-mcmc/lib"
+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB:/usr/lib" -cp "$BEAST_LIB/beast.jar:$BEAST_LIB/beast-beagle.jar" dr.app.beast.BeastMain $*
+Index: beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/beauti
+===================================================================
+--- beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/beauti 2011-01-24 16:39:49.000000000 +0000
++++ beast-mcmc-1.6.1+svnr3660/release/Linux/scripts/beauti 2011-01-24 16:40:13.000000000 +0000
+@@ -1,27 +1,5 @@
+ #!/bin/sh
+-if [ -z "$BEAST" ]; then
+- ## resolve links - $0 may be a link to application
+- PRG="$0"
+-
+- # need this for relative symlinks
+- while [ -h "$PRG" ] ; do
+- ls=`ls -ld "$PRG"`
+- link=`expr "$ls" : '.*-> \(.*\)$'`
+- if expr "$link" : '/.*' > /dev/null; then
+- PRG="$link"
+- else
+- PRG="`dirname "$PRG"`/$link"
+- fi
+- done
+-
+- # make it fully qualified
+- saveddir=`pwd`
+- BEAST0=`dirname "$PRG"`/..
+- BEAST=`cd "$BEAST0" && pwd`
+- cd "$saveddir"
+-fi
+-
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="/usr/share/beast-mcmc/lib"
+ java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -jar "$BEAST_LIB/beauti.jar" $*
+
+Index: beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/loganalyser
+===================================================================
+--- beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/loganalyser 2011-01-24 16:40:19.000000000 +0000
++++ beast-mcmc-1.6.1+svnr3660/release/Linux/scripts/loganalyser 2011-01-24 16:40:34.000000000 +0000
+@@ -1,27 +1,5 @@
+ #!/bin/sh
+
+-if [ -z "$BEAST" ]; then
+- ## resolve links - $0 may be a link to application
+- PRG="$0"
+-
+- # need this for relative symlinks
+- while [ -h "$PRG" ] ; do
+- ls=`ls -ld "$PRG"`
+- link=`expr "$ls" : '.*-> \(.*\)$'`
+- if expr "$link" : '/.*' > /dev/null; then
+- PRG="$link"
+- else
+- PRG="`dirname "$PRG"`/$link"
+- fi
+- done
+-
+- # make it fully qualified
+- saveddir=`pwd`
+- BEAST0=`dirname "$PRG"`/..
+- BEAST=`cd "$BEAST0" && pwd`
+- cd "$saveddir"
+-fi
+-
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="/usr/share/beast-mcmc/lib"
+ java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogAnalyser $*
+
+Index: beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/logcombiner
+===================================================================
+--- beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/logcombiner 2011-01-24 16:40:52.000000000 +0000
++++ beast-mcmc-1.6.1+svnr3660/release/Linux/scripts/logcombiner 2011-01-24 16:41:09.000000000 +0000
+@@ -1,27 +1,5 @@
+ #!/bin/sh
+
+-if [ -z "$BEAST" ]; then
+- ## resolve links - $0 may be a link to application
+- PRG="$0"
+-
+- # need this for relative symlinks
+- while [ -h "$PRG" ] ; do
+- ls=`ls -ld "$PRG"`
+- link=`expr "$ls" : '.*-> \(.*\)$'`
+- if expr "$link" : '/.*' > /dev/null; then
+- PRG="$link"
+- else
+- PRG="`dirname "$PRG"`/$link"
+- fi
+- done
+-
+- # make it fully qualified
+- saveddir=`pwd`
+- BEAST0=`dirname "$PRG"`/..
+- BEAST=`cd "$BEAST0" && pwd`
+- cd "$saveddir"
+-fi
+-
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="/usr/share/beast-mcmc/lib"
+ java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogCombiner $*
+
+Index: beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/treeannotator
+===================================================================
+--- beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/treeannotator 2011-01-24 16:41:21.000000000 +0000
++++ beast-mcmc-1.6.1+svnr3660/release/Linux/scripts/treeannotator 2011-01-24 16:41:41.000000000 +0000
+@@ -1,27 +1,5 @@
+ #!/bin/sh
+
+-if [ -z "$BEAST" ]; then
+- ## resolve links - $0 may be a link to application
+- PRG="$0"
+-
+- # need this for relative symlinks
+- while [ -h "$PRG" ] ; do
+- ls=`ls -ld "$PRG"`
+- link=`expr "$ls" : '.*-> \(.*\)$'`
+- if expr "$link" : '/.*' > /dev/null; then
+- PRG="$link"
+- else
+- PRG="`dirname "$PRG"`/$link"
+- fi
+- done
+-
+- # make it fully qualified
+- saveddir=`pwd`
+- BEAST0=`dirname "$PRG"`/..
+- BEAST=`cd "$BEAST0" && pwd`
+- cd "$saveddir"
+-fi
+-
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="/usr/share/beast-mcmc/lib"
+ java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.TreeAnnotator $*
+
+Index: beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/treestat
+===================================================================
+--- beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/treestat 2011-01-24 16:41:53.000000000 +0000
++++ beast-mcmc-1.6.1+svnr3660/release/Linux/scripts/treestat 2011-01-24 16:42:22.000000000 +0000
+@@ -1,27 +1,5 @@
+ #!/bin/sh
+
+-if [ -z "$BEAST" ]; then
+- ## resolve links - $0 may be a link to application
+- PRG="$0"
+-
+- # need this for relative symlinks
+- while [ -h "$PRG" ] ; do
+- ls=`ls -ld "$PRG"`
+- link=`expr "$ls" : '.*-> \(.*\)$'`
+- if expr "$link" : '/.*' > /dev/null; then
+- PRG="$link"
+- else
+- PRG="`dirname "$PRG"`/$link"
+- fi
+- done
+-
+- # make it fully qualified
+- saveddir=`pwd`
+- BEAST0=`dirname "$PRG"`/..
+- BEAST=`cd "$BEAST0" && pwd`
+- cd "$saveddir"
+-fi
+-
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="/usr/share/beast-mcmc/lib"
+ java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.treestat.TreeStatApp $*
+
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/series
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/series 2011-01-24 15:31:09 UTC (rev 5695)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/series 2011-01-24 16:50:26 UTC (rev 5696)
@@ -1,3 +1 @@
beast.patch
-native_flags.patch
-fix_paths.patch
Modified: trunk/packages/beast-mcmc/trunk/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/rules 2011-01-24 15:31:09 UTC (rev 5695)
+++ trunk/packages/beast-mcmc/trunk/debian/rules 2011-01-24 16:50:26 UTC (rev 5696)
@@ -53,8 +53,8 @@
build-stamp: patch
dh_testdir
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml build_jar_all_BEAST_NoJUnitTest
- cd native && make linux
+ $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml build
+ cd native && /bin/sh compileNativeLinux.sh
touch build-stamp
binary-indep: build-indep install
@@ -88,19 +88,20 @@
dh_gencontrol
dh_md5sums
#dh_builddeb
- mv $(CURDIR)/scripts/beast $(CURDIR)/scripts/beast-mcmc
- install $(CURDIR)/scripts/beast-mcmc $(CURDIR)/debian/beast-mcmc/usr/bin/
- install $(CURDIR)/scripts/beauti $(CURDIR)/debian/beast-mcmc/usr/bin/
- install $(CURDIR)/scripts/loganalyser $(CURDIR)/debian/beast-mcmc/usr/bin/
- install $(CURDIR)/scripts/logcombiner $(CURDIR)/debian/beast-mcmc/usr/bin/
- install $(CURDIR)/scripts/treeannotator $(CURDIR)/debian/beast-mcmc/usr/bin/
+ mv $(CURDIR)/release/Linux/scripts/beast $(CURDIR)/release/Linux/scripts/beast-mcmc
+ install $(CURDIR)/release/Linux/scripts/beast-mcmc $(CURDIR)/debian/beast-mcmc/usr/bin/
+ install $(CURDIR)/release/Linux/scripts/beauti $(CURDIR)/debian/beast-mcmc/usr/bin/
+ install $(CURDIR)/release/Linux/scripts/loganalyser $(CURDIR)/debian/beast-mcmc/usr/bin/
+ install $(CURDIR)/release/Linux/scripts/logcombiner $(CURDIR)/debian/beast-mcmc/usr/bin/
+ install $(CURDIR)/release/Linux/scripts/treeannotator $(CURDIR)/debian/beast-mcmc/usr/bin/
+ install $(CURDIR)/release/Linux/scripts/treestat $(CURDIR)/debian/beast-mcmc/usr/bin/
install -m 664 $(CURDIR)/lib/*\.jar $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/lib
install -m 664 $(CURDIR)/build/dist/*\.jar $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/lib
install -m 664 $(CURDIR)/native/*\.so $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/lib
install -m 664 $(CURDIR)/release/common/icons/beast.png $(CURDIR)/debian/beast-mcmc/usr/share/pixmaps/
install -m 664 $(CURDIR)/doc/*pdf $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/doc
install -m 664 $(CURDIR)/doc/Virus\ Practical\ Tex/*pdf $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/doc
- install -m 664 $(CURDIR)/examples/*\.xml $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/examples
+ install -m 664 $(CURDIR)/examples/release/*\.xml $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/examples
dh_desktop
dh_installmenu
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