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Copy pathbf.sh
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executable file
·78 lines (68 loc) · 2.06 KB
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#!/usr/bin/env bash
# bf.sh: the script that actually launches a command line tool
BF_DIR=`dirname "$0"`
# Include the master configuration file.
source "$BF_DIR/config.sh"
# Check that a command to run was specified.
if [ -z "$BF_PROG" ]
then
echo The command to launch must be set in the BF_PROG environment variable.
exit 1
fi
# Prepare the flags.
if [ -z "$BF_FLAGS" ]
then
BF_FLAGS=""
fi
# Set the max heap size.
if [ -z "$BF_MAX_MEM" ]
then
# Set a reasonable default max heap size.
BF_MAX_MEM="512m"
fi
BF_FLAGS="$BF_FLAGS -Xmx$BF_MAX_MEM"
# Skip the update check if the NO_UPDATE_CHECK flag is set.
if [ -n "$NO_UPDATE_CHECK" ]
then
BF_FLAGS="$BF_FLAGS -Dbioformats_can_do_upgrade_check=false"
fi
# Run profiling if the BF_PROFILE flag is set.
if [ -n "$BF_PROFILE" ]
then
# Set default profiling depth
if [ -z "$BF_PROFILE_DEPTH" ]
then
BF_PROFILE_DEPTH="30"
fi
BF_FLAGS="$BF_FLAGS -agentlib:hprof=cpu=samples,depth=$BF_PROFILE_DEPTH,file=$BF_PROG.hprof"
fi
# Use any available proxy settings.
BF_FLAGS="$BF_FLAGS -Dhttp.proxyHost=$PROXY_HOST -Dhttp.proxyPort=$PROXY_PORT"
# Run the command!
if [ -n "$BF_DEVEL" ]
then
# Developer environment variable set; launch with existing classpath.
java $BF_FLAGS $BF_PROG "$@"
else
# Developer environment variable unset; add JAR libraries to classpath.
if [ -e "$BF_JAR_DIR/bioformats_package.jar" ]
then
BF_CP="$BF_JAR_DIR/bioformats_package.jar:$BF_CP"
elif [ -e "$BF_JAR_DIR/formats-gpl.jar" ]
then
BF_CP="$BF_JAR_DIR/formats-gpl.jar:$BF_JAR_DIR/bio-formats-tools.jar:$BF_CP"
else
# Libraries not found; issue an error.
echo "Required JAR libraries not found. Please download:"
echo " bioformats_package.jar"
echo "from:"
echo " https://downloads.openmicroscopy.org/latest/bio-formats/artifacts/"
echo "and place in the same directory as the command line tools."
exit 2
fi
if [ -e "$BF_JAR_DIR/bio-formats-testing-framework.jar" ]
then
BF_CP="$BF_CP:$BF_JAR_DIR/bio-formats-testing-framework.jar"
fi
java $BF_FLAGS -cp "$BF_DIR:$BF_CP" $BF_PROG "$@"
fi