/usr/bin/beauti2 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 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 | #!/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/
if echo $@ | grep -q -- -template ; then
TEMPLATE=""
else
TEMPLATE="-template ${BEAST_LIB}/templates/Standard.xml"
fi
if [ "$https_proxy" != "" ] ; then
HTTPSPROXYHOST=`echo $https_proxy | sed -e 's?^https*:/*??' -e 's/:[0-9]*//'`
HTTPSPROXYPORT=`echo $https_proxy | sed -e 's/^.*:\([0-9]\+\)$/\1/'`
SETHTTPS="-Dhttps.proxyHost=${HTTPSPROXYHOST} -Dhttps.proxyPort=${HTTPSPROXYPORT}"
fi
if [ "$http_proxy" != "" ] ; then
HTTPPROXYHOST=`echo $http_proxy | sed -e 's?^http:/*??' -e 's/:[0-9]*//'`
HTTPPROXYPORT=`echo $http_proxy | sed -e 's/^.*:\([0-9]\+\)$/\1/'`
SETHTTP="-Dhttp.proxyHost=${HTTPPROXYHOST} -Dhttp.proxyPort=${HTTPPROXYPORT}"
if [ "$SETHTTPS" = "" ] ; then
SETHTTPS="-Dhttps.proxyHost=${HTTPPROXYHOST} -Dhttps.proxyPort=${HTTPPROXYPORT}"
fi
fi
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" $SETHTTP $SETHTTPS \
-classpath "${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 \
${TEMPLATE} $*
|