[med-svn] [beast2-mcmc] 02/03: Try to get some working wrappers - testing needed
Andreas Tille
tille at debian.org
Tue Oct 6 13:14:24 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 269a621e8f5b60f847f547ce62b8976d7e7665d2
Author: Andreas Tille <tille at debian.org>
Date: Tue Oct 6 15:13:11 2015 +0200
Try to get some working wrappers - testing needed
---
debian/beast2-mcmc.install | 3 ++-
debian/beast2-mcmc.manifest | 8 ++++++--
debian/bin/beast-mcmc2 | 7 ++++---
debian/bin/beauti | 5 -----
debian/bin/{beast-mcmc2 => beauti2} | 7 ++++---
debian/bin/loganalyser | 5 -----
debian/bin/logcombiner | 7 -------
debian/bin/treeannotator | 9 ---------
debian/bin/{beast-mcmc2 => treeannotator2} | 7 ++++---
debian/bin/treestat | 8 --------
10 files changed, 20 insertions(+), 46 deletions(-)
diff --git a/debian/beast2-mcmc.install b/debian/beast2-mcmc.install
index ebbc5e2..95e6fce 100644
--- a/debian/beast2-mcmc.install
+++ b/debian/beast2-mcmc.install
@@ -1,2 +1,3 @@
debian/bin usr
-build/dist/*.jar usr/share/beast-mcmc2
+build/dist/beast.jar usr/share/beast-mcmc2
+build/dist/launcher.jar usr/share/beast-mcmc2
diff --git a/debian/beast2-mcmc.manifest b/debian/beast2-mcmc.manifest
index 521411b..e800184 100644
--- a/debian/beast2-mcmc.manifest
+++ b/debian/beast2-mcmc.manifest
@@ -1,3 +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
+ Main-Class: beast.app.beastapp.BeastMain
+ Class-Path: /usr/share/java/beagle.jar /usr/share/java/commons-math.jar /usr/share/java/jam.jar /usr/share/beast-mcmc2/beast.jar
+
+/usr/share/beast-mcmc2/launcher.jar:
+ Main-Class: beast.app.beauti.BeautiLauncher
+ Class-Path: /usr/share/java/beagle.jar /usr/share/java/commons-math.jar /usr/share/java/jam.jar /usr/share/beast-mcmc2/beast.jar
diff --git a/debian/bin/beast-mcmc2 b/debian/bin/beast-mcmc2
index 2dea939..6478054 100644
--- a/debian/bin/beast-mcmc2
+++ b/debian/bin/beast-mcmc2
@@ -23,6 +23,7 @@ MAXMEM=3072
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 $*
+JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64/"
+${JAVA_HOME}/bin/java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="$BEAST_LIB" \
+ -classpath "${CLASSPATH}:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/jdom1.jar:${DEBJAR}/colt.jar:${DEBJAR}/commons-math.jar:${BEAST_LIB}/beast.jar:$BEAST_LIB/launcher.jar" \
+ beast.app.beastapp.BeastLauncher $*
diff --git a/debian/bin/beauti b/debian/bin/beauti
deleted file mode 100644
index d2fe574..0000000
--- a/debian/bin/beauti
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-
-BEAST_LIB="/usr/share/beast-mcmc2"
-java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -jar "$BEAST_LIB/beauti.jar" $*
-
diff --git a/debian/bin/beast-mcmc2 b/debian/bin/beauti2
similarity index 82%
copy from debian/bin/beast-mcmc2
copy to debian/bin/beauti2
index 2dea939..c51d2f6 100644
--- a/debian/bin/beast-mcmc2
+++ b/debian/bin/beauti2
@@ -23,6 +23,7 @@ MAXMEM=3072
BEAST_LIB="/usr/share/beast-mcmc2"
DEBJAR="/usr/share/java"
-java -Xms64m -Xmx${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 $*
+JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64/"
+${JAVA_HOME}/bin/java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="$BEAST_LIB" \
+ -classpath "${CLASSPATH}:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/jdom1.jar:${DEBJAR}/colt.jar:${DEBJAR}/commons-math.jar:${BEAST_LIB}/beast.jar:$BEAST_LIB/launcher.jar" \
+ beast.app.beauti.BeautiLauncher $*
diff --git a/debian/bin/loganalyser b/debian/bin/loganalyser
deleted file mode 100644
index 047c863..0000000
--- a/debian/bin/loganalyser
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-
-BEAST_LIB="/usr/share/beast-mcmc2"
-java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogAnalyser $*
-
diff --git a/debian/bin/logcombiner b/debian/bin/logcombiner
deleted file mode 100644
index 823a270..0000000
--- a/debian/bin/logcombiner
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/sh
-
-BEAST_LIB="/usr/share/beast-mcmc2"
-DEBJAR="/usr/share/java"
-java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
- -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \
- dr.app.tools.LogCombiner $*
diff --git a/debian/bin/treeannotator b/debian/bin/treeannotator
deleted file mode 100644
index fd6efb3..0000000
--- a/debian/bin/treeannotator
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/sh
-
-BEAST_LIB="/usr/share/beast-mcmc2"
-DEBJAR="/usr/share/java"
-java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
- -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \
- dr.app.tools.TreeAnnotator $*
-
-
diff --git a/debian/bin/beast-mcmc2 b/debian/bin/treeannotator2
similarity index 82%
copy from debian/bin/beast-mcmc2
copy to debian/bin/treeannotator2
index 2dea939..5bc240d 100644
--- a/debian/bin/beast-mcmc2
+++ b/debian/bin/treeannotator2
@@ -23,6 +23,7 @@ MAXMEM=3072
BEAST_LIB="/usr/share/beast-mcmc2"
DEBJAR="/usr/share/java"
-java -Xms64m -Xmx${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 $*
+JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64/"
+${JAVA_HOME}/bin/java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="$BEAST_LIB" \
+ -classpath "${CLASSPATH}:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/jdom1.jar:${DEBJAR}/colt.jar:${DEBJAR}/commons-math.jar:${BEAST_LIB}/beast.jar:$BEAST_LIB/launcher.jar" \
+ beast.app.treeannotator.TreeAnnotatorLauncher $*
diff --git a/debian/bin/treestat b/debian/bin/treestat
deleted file mode 100644
index 2686a78..0000000
--- a/debian/bin/treestat
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/sh
-
-BEAST_LIB="/usr/share/beast-mcmc2"
-DEBJAR="/usr/share/java"
-java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
- -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar:${DEBJAR}/jdom1.jar \
- dr.app.treestat.TreeStatApp $*
-
--
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