154 lines
5.8 KiB
Bash
Executable File
154 lines
5.8 KiB
Bash
Executable File
#!/bin/bash
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#
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# Copyright 2013-2026, Seqera Labs
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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#set -e
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#set -u
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#set -o errexit
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function resolve_link() {
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[[ ! -f $1 ]] && exit 1
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if command -v realpath &>/dev/null; then
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realpath "$1"
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elif command -v readlink &>/dev/null; then
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local target="$1"
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cd $(dirname $target); target=$(basename $target)
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while [ -L "$target" ]; do
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target="$(readlink "$target")"
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cd $(dirname $target); target=$(basename $target)
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done
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echo "$(cd "$(dirname "$target")"; pwd -P)/$target"
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else
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echo_yellow "WARN: Neither \`realpath\` nor \`readlink\` command can be found"
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exit 1
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fi
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}
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# the application 'base' folder
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bin_dir=`dirname $(resolve_link $0)`
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base_dir=$bin_dir
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# define the java env
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JAVA_BIN=java
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if test -n "$JAVA_HOME"; then
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JAVA_BIN="$JAVA_HOME/bin/java"
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fi
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#
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# debugging JVM options
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# export _JAVA_OPTIONS='-Xms1g -Xmx2g -verbose:gc -XX:+AggressiveOpts -XX:+UnlockDiagnosticVMOptions -XX:+UnlockExperimentalVMOptions -XX:+PrintFlagsFinal -XX:+TraceClassLoading -XX:+TraceClassUnloading -verbose:class'
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#
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#
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# Variable definition
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#
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declare -a args=()
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DEBUG=''
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COLUMNS=${COLUMNS:-`tput cols 2>/dev/null || echo 80`}
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MAIN_CLASS=${MAIN_CLASS:-'nextflow.cli.Launcher'}
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JAVA_VER="$($JAVA_BIN -version 2>&1)"
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if [ $? -ne 0 ]; then
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echo "${JAVA_VER:-Failed to launch the Java virtual machine}"
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exit 1
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fi
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JAVA_VER=$(echo "$JAVA_VER" | awk '/version/ {gsub(/"/, "", $3); print $3}')
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major=${BASH_REMATCH[1]}
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minor=${BASH_REMATCH[2]}
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version_check="^(17|18|19|20|21|22|23|24|25|26)"
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if [[ ! $JAVA_VER =~ $version_check ]]; then
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echo "Error: cannot find Java or it's a wrong version -- please make sure that Java 17 or higher is installed"
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exit 1
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fi
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JVM_ARGS+=" -Dfile.encoding=UTF-8 -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
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JVM_ARGS+=" --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/java.nio.file.spi=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED --add-opens=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/sun.nio.fs=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED --add-opens=java.base/jdk.internal.misc=ALL-UNNAMED --add-opens=java.base/jdk.internal.vm=ALL-UNNAMED --add-opens=java.base/java.util.regex=ALL-UNNAMED"
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[[ "$JAVA_VER" =~ ^(24|25|26) ]]&& JVM_ARGS+=" --enable-native-access=ALL-UNNAMED --sun-misc-unsafe-memory-access=allow"
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[[ $NXF_ENABLE_VIRTUAL_THREADS == 'true' ]] && [[ "$JAVA_VER" =~ ^(19|20) ]] && JVM_ARGS+=" --enable-preview"
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[[ "$JAVA_VER" =~ ^(21) ]] && [[ ! "$NXF_ENABLE_VIRTUAL_THREADS" ]] && NXF_ENABLE_VIRTUAL_THREADS=true
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## flight recorded -- http://docs.oracle.com/javacomponents/jmc-5-4/jfr-runtime-guide/run.htm
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##JVM_ARGS+=" -XX:+UnlockCommercialFeatures -XX:+FlightRecorder -XX:StartFlightRecording=duration=60s,filename=myrecording.jfr"
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NXF_PLUGINS_DIR=${NXF_PLUGINS_DIR:-$base_dir/plugins}
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NXF_PLUGINS_MODE=${NXF_PLUGINS_MODE:-dev}
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NXF_PLUGINS_DEFAULT=${NXF_PLUGINS_DEFAULT:-true}
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NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
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NXF_OPTS=${NXF_OPTS:-}
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NXF_CLI="$0 $@"
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NXF_REMOTE_DEBUG_PORT=${NXF_REMOTE_DEBUG_PORT:-5005}
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export NXF_CLI
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export COLUMNS
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export NXF_PLUGINS_DIR
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export NXF_PLUGINS_MODE
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export NXF_PLUGINS_DEFAULT
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export NXF_ENABLE_VIRTUAL_THREADS
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# Yourkit profiling library
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YOURKIT_AGENT=${YOURKIT_AGENT:-/Applications/YourKit-Java-Profiler-2021.11.app/Contents/Resources/bin/mac/libyjpagent.dylib}
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#
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# classpath when the application is compiled with gradle
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#
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[[ ! -f "$base_dir/.launch.classpath" ]] && echo "Missing '.launch.classpath' file -- create it by running: ./gradlew exportClasspath" && exit 1
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CLASSPATH+=":`cat $base_dir/.launch.classpath`"
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#
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# Handle special program cli options
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#
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while [ "$*" != "" ]; do
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if [[ "$1" == '-debug' || "$1" == '-trace' ]]; then
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args+=("$1")
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elif [ "$1" == --yourkit ]; then
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JVM_ARGS+=" -agentpath:$YOURKIT_AGENT "
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elif [ "$1" == '--with-jrebel' ]; then
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if [ "$JREBEL_HOME" ]; then
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JVM_ARGS+=" -javaagent:$JREBEL_HOME/jrebel.jar -Drebel.log.file=./jrebel-client.log"
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else
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echo "WARN: To use JRebel define the JREBEL_HOME variable in environment"
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fi
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elif [ "$1" == '-remote-debug' ]; then
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DEBUG="-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=$NXF_REMOTE_DEBUG_PORT"
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args+=("$1")
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elif [ "$1" == '-enable-checkpoint' ]; then
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mkdir -p crac-files
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JVM_ARGS+=" -XX:CRaCCheckpointTo=$PWD/crac-files"
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elif [ "$1" == '-checkpoint' ]; then
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jcmd $CLASSPATH JDK.checkpoint
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exit 0
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else
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args+=("$1")
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fi
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# move to the next option
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shift
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done
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# Show some variable when in DEBUG mode
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if [ "$DEBUG" != '' ]; then
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echo Launch environment
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echo ------------------
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echo base_dir: $base_dir
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echo jvmargs: $JVM_ARGS
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echo debug: $DEBUG
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echo classpath:
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echo $CLASSPATH | tr ":" "\n" | sort
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echo ''
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echo Launching it!
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echo ------------------
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fi
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# Launch the APP
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exec $JAVA_BIN $JVM_ARGS $DEBUG $NXF_OPTS -cp "$CLASSPATH" "$MAIN_CLASS" "${args[@]}"
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