Author: tille Date: 2012-01-11 16:11:15 +0000 (Wed, 11 Jan 2012) New Revision: 9252
Added: trunk/packages/beast-mcmc/trunk/debian/bin/ trunk/packages/beast-mcmc/trunk/debian/bin/beast-mcmc trunk/packages/beast-mcmc/trunk/debian/bin/beauti trunk/packages/beast-mcmc/trunk/debian/bin/loganalyser trunk/packages/beast-mcmc/trunk/debian/bin/logcombiner trunk/packages/beast-mcmc/trunk/debian/bin/treeannotator trunk/packages/beast-mcmc/trunk/debian/bin/treestat Removed: trunk/packages/beast-mcmc/trunk/debian/README.source trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch trunk/packages/beast-mcmc/trunk/debian/patches/some_bins_need_explicit_classpath.patch Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest trunk/packages/beast-mcmc/trunk/debian/control trunk/packages/beast-mcmc/trunk/debian/patches/series trunk/packages/beast-mcmc/trunk/debian/rules Log: Do not try to patch singular upstream wrappers if we need to do massive changes to work around stupid manifest problems anyway it makes sense to provide them directly in debian/bin Deleted: trunk/packages/beast-mcmc/trunk/debian/README.source =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/README.source 2012-01-11 15:52:48 UTC (rev 9251) +++ trunk/packages/beast-mcmc/trunk/debian/README.source 2012-01-11 16:11:15 UTC (rev 9252) @@ -1,10 +0,0 @@ -The beast-mcmc source is not provided as tarball but only in SVN. -The SVN revision was tagged a 1.6.1 as it can be seen at - - http://code.google.com/p/beast-mcmc/source/detail?r=3660 - -The script debian/get-orig-source fetches exactly this revision. -In addition it removes some binary jars which are packaged for -Debian and do not need to be shipped with the original tarball. - - -- Andreas Tille <[email protected]> Tue, 15 Feb 2011 12:39:04 +0100 \ No newline at end of file Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install 2012-01-11 15:52:48 UTC (rev 9251) +++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install 2012-01-11 16:11:15 UTC (rev 9252) @@ -1,4 +1,4 @@ -release/Linux/scripts/* usr/bin -debian/*.xpm usr/share/pixmaps -lib/*.jar usr/share/beast-mcmc -build/dist/*.jar usr/share/beast-mcmc +debian/bin usr +debian/*.xpm usr/share/pixmaps +lib/*.jar usr/share/beast-mcmc +build/dist/*.jar usr/share/beast-mcmc Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest 2012-01-11 15:52:48 UTC (rev 9251) +++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest 2012-01-11 16:11:15 UTC (rev 9252) @@ -1,6 +1,6 @@ /usr/share/beast-mcmc/beast.jar: Main-Class: dr.app.beast.BeastMain - Class-Path: /usr/share/beast-mcmc/beagle.jar /usr/share/java/jebl.jar /usr/share/java/jam.jar /usr/share/java/treeview.jar + Class-Path: /usr/share/beast-mcmc/beagle.jar /usr/share/java/commons-math.jar /usr/share/java/jdom1.jar /usr/share/java/jebl.jar /usr/share/java/jam.jar /usr/share/java/treeview.jar /usr/share/beast-mcmc/beauti.jar: Main-Class: dr.app.beauti.BeautiApp Added: trunk/packages/beast-mcmc/trunk/debian/bin/beast-mcmc =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/bin/beast-mcmc (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/bin/beast-mcmc 2012-01-11 16:11:15 UTC (rev 9252) @@ -0,0 +1,15 @@ +#!/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 + +BEAST_LIB="/usr/share/beast-mcmc" +DEBJAR="/usr/share/java" +java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="$BEAST_LIB:/usr/lib" \ + -classpath "${CLASSPATH}:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/jdom1.jar:${DEBJAR}/commons-math.jar:${DEBJAR}/treeview.jar:${BEAST_LIB}/beast.jar:$BEAST_LIB/beast-beagle.jar" \ + dr.app.beast.BeastMain $* Added: trunk/packages/beast-mcmc/trunk/debian/bin/beauti =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/bin/beauti (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/bin/beauti 2012-01-11 16:11:15 UTC (rev 9252) @@ -0,0 +1,5 @@ +#!/bin/sh + +BEAST_LIB="/usr/share/beast-mcmc" +java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -jar "$BEAST_LIB/beauti.jar" $* + Added: trunk/packages/beast-mcmc/trunk/debian/bin/loganalyser =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/bin/loganalyser (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/bin/loganalyser 2012-01-11 16:11:15 UTC (rev 9252) @@ -0,0 +1,5 @@ +#!/bin/sh + +BEAST_LIB="/usr/share/beast-mcmc" +java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogAnalyser $* + Added: trunk/packages/beast-mcmc/trunk/debian/bin/logcombiner =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/bin/logcombiner (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/bin/logcombiner 2012-01-11 16:11:15 UTC (rev 9252) @@ -0,0 +1,7 @@ +#!/bin/sh + +BEAST_LIB="/usr/share/beast-mcmc" +DEBJAR="/usr/share/java" +java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \ + -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \ + dr.app.tools.LogCombiner $* Added: trunk/packages/beast-mcmc/trunk/debian/bin/treeannotator =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/bin/treeannotator (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/bin/treeannotator 2012-01-11 16:11:15 UTC (rev 9252) @@ -0,0 +1,9 @@ +#!/bin/sh + +BEAST_LIB="/usr/share/beast-mcmc" +DEBJAR="/usr/share/java" +java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \ + -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \ + dr.app.tools.TreeAnnotator $* + + Added: trunk/packages/beast-mcmc/trunk/debian/bin/treestat =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/bin/treestat (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/bin/treestat 2012-01-11 16:11:15 UTC (rev 9252) @@ -0,0 +1,8 @@ +#!/bin/sh + +BEAST_LIB="/usr/share/beast-mcmc" +DEBJAR="/usr/share/java" +java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \ + -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar:${DEBJAR}/jdom1.jar \ + dr.app.treestat.TreeStatApp $* + Modified: trunk/packages/beast-mcmc/trunk/debian/control =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/control 2012-01-11 15:52:48 UTC (rev 9251) +++ trunk/packages/beast-mcmc/trunk/debian/control 2012-01-11 16:11:15 UTC (rev 9252) @@ -18,7 +18,8 @@ Package: beast-mcmc Architecture: all -Depends: ${shlibs:Depends}, ${misc:Depends}, openjdk-6-jre | java-jre, beast-mcmc-lib, xterm | x-terminal-emulator +Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}, openjdk-6-jre | java-jre, + beast-mcmc-lib, xterm | x-terminal-emulator Suggests: beast-doc Description: Bayesian MCMC phylogenetic inference BEAST is a cross-platform program for Bayesian MCMC analysis of molecular @@ -87,4 +88,3 @@ analyses and a suit of programs for analysing the results. . This package contains the documentation. - Deleted: trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch 2012-01-11 15:52:48 UTC (rev 9251) +++ trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch 2012-01-11 16:11:15 UTC (rev 9252) @@ -1,186 +0,0 @@ ---- beast-mcmc-1.6.2.orig/release/Linux/scripts/beast -+++ beast-mcmc-1.6.2/release/Linux/scripts/beast -@@ -1,26 +1,4 @@ - #!/bin/sh - --if [ -z "$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="$BEAST/lib" --java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB:/usr/local/lib" -cp "$BEAST_LIB/beast.jar:$BEAST_LIB/beast-beagle.jar" dr.app.beast.BeastMain $* -+BEAST_LIB="/usr/share/beast-mcmc" -+java -Xms64m -Xmx2048m -Djava.library.path="$BEAST_LIB:/usr/lib" -cp "$BEAST_LIB/beast.jar:$BEAST_LIB/beast-beagle.jar" dr.app.beast.BeastMain $* ---- beast-mcmc-1.6.2.orig/release/Linux/scripts/beauti -+++ beast-mcmc-1.6.2/release/Linux/scripts/beauti -@@ -1,27 +1,5 @@ - #!/bin/sh - --if [ -z "$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="$BEAST/lib" -+BEAST_LIB="/usr/share/beast-mcmc" - java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -jar "$BEAST_LIB/beauti.jar" $* - ---- beast-mcmc-1.6.2.orig/release/Linux/scripts/loganalyser -+++ beast-mcmc-1.6.2/release/Linux/scripts/loganalyser -@@ -1,27 +1,5 @@ - #!/bin/sh - --if [ -z "$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="$BEAST/lib" -+BEAST_LIB="/usr/share/beast-mcmc" - java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogAnalyser $* - ---- beast-mcmc-1.6.2.orig/release/Linux/scripts/logcombiner -+++ beast-mcmc-1.6.2/release/Linux/scripts/logcombiner -@@ -1,27 +1,5 @@ - #!/bin/sh - --if [ -z "$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="$BEAST/lib" -+BEAST_LIB="/usr/share/beast-mcmc" - java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogCombiner $* - ---- beast-mcmc-1.6.2.orig/release/Linux/scripts/treeannotator -+++ beast-mcmc-1.6.2/release/Linux/scripts/treeannotator -@@ -1,27 +1,5 @@ - #!/bin/sh - --if [ -z "$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="$BEAST/lib" -+BEAST_LIB="/usr/share/beast-mcmc" - java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.TreeAnnotator $* - ---- beast-mcmc-1.6.2.orig/release/Linux/scripts/treestat -+++ beast-mcmc-1.6.2/release/Linux/scripts/treestat -@@ -1,27 +1,5 @@ - #!/bin/sh - --if [ -z "$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="$BEAST/lib" -+BEAST_LIB="/usr/share/beast-mcmc" - java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.treestat.TreeStatApp $* - Modified: trunk/packages/beast-mcmc/trunk/debian/patches/series =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/series 2012-01-11 15:52:48 UTC (rev 9251) +++ trunk/packages/beast-mcmc/trunk/debian/patches/series 2012-01-11 16:11:15 UTC (rev 9252) @@ -1,6 +1,4 @@ -beast.patch fix_gcc_options.patch fix_classpath_in_build_xml.patch patch_tex_docs.patch fix_classpath_in_build_tracer_xml.patch -some_bins_need_explicit_classpath.patch Deleted: trunk/packages/beast-mcmc/trunk/debian/patches/some_bins_need_explicit_classpath.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/some_bins_need_explicit_classpath.patch 2012-01-11 15:52:48 UTC (rev 9251) +++ trunk/packages/beast-mcmc/trunk/debian/patches/some_bins_need_explicit_classpath.patch 2012-01-11 16:11:15 UTC (rev 9252) @@ -1,42 +0,0 @@ -Author: Andreas Tille <[email protected]> -Description: The scripts logcombiner, treeannotator and treestat - did not run without explicite CLASSPATH setting. This is done - in this patch - ---- beast-mcmc-1.6.2.orig/release/Linux/scripts/logcombiner -+++ beast-mcmc-1.6.2/release/Linux/scripts/logcombiner -@@ -1,5 +1,7 @@ - #!/bin/sh - - BEAST_LIB="/usr/share/beast-mcmc" --java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogCombiner $* -- -+DEBJAR="/usr/share/java" -+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \ -+ -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \ -+ dr.app.tools.LogCombiner $* ---- beast-mcmc-1.6.2.orig/release/Linux/scripts/treeannotator -+++ beast-mcmc-1.6.2/release/Linux/scripts/treeannotator -@@ -1,5 +1,9 @@ - #!/bin/sh - - BEAST_LIB="/usr/share/beast-mcmc" --java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.TreeAnnotator $* -+DEBJAR="/usr/share/java" -+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \ -+ -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \ -+ dr.app.tools.TreeAnnotator $* -+ - ---- beast-mcmc-1.6.2.orig/release/Linux/scripts/treestat -+++ beast-mcmc-1.6.2/release/Linux/scripts/treestat -@@ -1,5 +1,8 @@ - #!/bin/sh - - BEAST_LIB="/usr/share/beast-mcmc" --java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.treestat.TreeStatApp $* -+DEBJAR="/usr/share/java" -+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \ -+ -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar:${DEBJAR}/jdom1.jar \ -+ dr.app.treestat.TreeStatApp $* - Modified: trunk/packages/beast-mcmc/trunk/debian/rules =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/rules 2012-01-11 15:52:48 UTC (rev 9251) +++ trunk/packages/beast-mcmc/trunk/debian/rules 2012-01-11 16:11:15 UTC (rev 9252) @@ -65,11 +65,6 @@ # # $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml junit -override_dh_install: - dh_install - # rename beast to beast-mcmc - mv $(CURDIR)/debian/$(PACKAGE)/usr/bin/beast $(CURDIR)/debian/$(PACKAGE)/usr/bin/beast-mcmc - override_dh_compress: dh_compress --exclude=.pdf _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
