/usr/bin/treeannotator2 is in beast2-mcmc 2.4.4+dfsg-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | #!/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_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 $*
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