504 lines
17 KiB
Bash
Executable File
504 lines
17 KiB
Bash
Executable File
#!/usr/bin/env 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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[[ "$NXF_DEBUG" == 'x' ]] && set -x
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NXF_VER=${NXF_VER:-'26.04.0'}
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NXF_ORG=${NXF_ORG:-'nextflow-io'}
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NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
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NXF_PROT=${NXF_PROT:-'https'}
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NXF_BASE=${NXF_BASE:-$NXF_PROT://www.nextflow.io/releases}
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NXF_TEMP=${NXF_TEMP:-$TMPDIR}
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NXF_DIST=${NXF_DIST:-$NXF_HOME/framework}
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NXF_CLI="$0 $@"
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NXF_CLI_OPTS=${NXF_CLI_OPTS:-}
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NXF_REMOTE_DEBUG_PORT=${NXF_REMOTE_DEBUG_PORT:-5005}
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function cmp_ver() {
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local IFS=.
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local i ver1 ver2
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read -r -a ver1 <<< "${1//./ }"
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read -r -a ver2 <<< "${2//./ }"
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# Compare major, minor, and patch numbers
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for ((i=0; i<3; i++)); do
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ver1[i]=${ver1[i]//[^0-9]}
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ver2[i]=${ver2[i]//[^0-9]}
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[[ ${ver1[i]:-0} -lt ${ver2[i]:-0} ]] && echo -1 && return
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[[ ${ver1[i]:-0} -gt ${ver2[i]:-0} ]] && echo 1 && return
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done
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# Extract suffixes for comparison
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local suffix1="${1##*.}"
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local suffix2="${2##*.}"
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suffix1="${suffix1//[0-9]}"
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suffix2="${suffix2//[0-9]}"
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# Compare suffixes
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[[ -z $suffix1 && -n $suffix2 ]] && echo 1 && return
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[[ -n $suffix1 && -z $suffix2 ]] && echo -1 && return
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[[ $suffix1 < $suffix2 ]] && echo -1 && return
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[[ $suffix1 > $suffix2 ]] && echo 1 && return
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# Versions are equal
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echo 0
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}
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# if the nextflow version is greater or equals to "24.07.0-edge" the new shadow jar launcher
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# should be used, otherwise fallback on the legacy behavior setting the variable NXF_LEGACY_LAUNCHER
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NXF_LEGACY_LAUNCHER=1
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if [[ $(cmp_ver "$NXF_VER" "24.07.0-edge") -ge 0 ]]; then
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unset NXF_LEGACY_LAUNCHER
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fi
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export NXF_CLI
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export NXF_ORG
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export NXF_HOME
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if [[ $TERM && $TERM != 'dumb' ]]; then
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if command -v tput &>/dev/null; then
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GREEN=$(tput setaf 2; tput bold)
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YELLOW=$(tput setaf 3)
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RED=$(tput setaf 1)
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NORMAL=$(tput sgr0)
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fi
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fi
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function echo_red() {
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>&2 echo -e "$RED$*$NORMAL"
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}
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function echo_green() {
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echo -e "$GREEN$*$NORMAL"
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}
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function echo_yellow() {
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>&2 echo -e "$YELLOW$*$NORMAL"
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}
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function die() {
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echo_red "$*"
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exit 1
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}
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function get_abs_filename() {
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echo "$(cd "$(dirname "$1")" && pwd)/$(basename "$1")"
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}
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function get() {
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if command -v curl &>/dev/null; then
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GET="curl -fsSL '$1' -o '$2'"
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elif command -v wget &>/dev/null; then
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GET="wget '$1' -O '$2' >/dev/null 2>&1"
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else
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echo_red "ERROR: Cannot find 'curl' nor 'wget' utility -- please install one of them"
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exit 1
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fi
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printf "Downloading nextflow dependencies. It may require a few seconds, please wait .. "
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eval $GET; status=$?
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printf "\r\033[K"
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if [ $status -ne 0 ]; then
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echo_red "ERROR: Cannot download nextflow required file -- make sure you can connect to the internet"
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echo ""
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echo "Alternatively you can try to download this file:"
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echo " $1"
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echo ""
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echo "and save it as:"
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echo " ${3:-$2}"
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echo ""
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exit 1
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fi
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}
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function get_ver() {
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if command -v curl &>/dev/null; then
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curl -fsSL "$1"
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elif command -v wget &>/dev/null; then
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wget "$1" >/dev/null 2>&1
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else
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echo_red "ERROR: Cannot find 'curl' nor 'wget' utility -- please install one of them"
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exit 1
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fi
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}
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function make_temp() {
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local base=${NXF_TEMP:=$PWD}
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if [ "$(uname)" = 'Darwin' ]; then mktemp "${base}/nxf-tmp.XXXXXX" || exit $?
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else mktemp -t nxf-tmp.XXXXXX -p "${base}" || exit $?
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fi
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}
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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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function current_ver() {
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[[ $NXF_EDGE == 1 || $NXF_VER == *"-edge" ]] && printf 'edge' || printf 'latest'
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}
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function install() {
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local tmpfile=$(make_temp)
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local version=$(set +u; [[ $NXF_VER ]] && printf "v$NXF_VER" || current_ver)
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local action="a=${2:-default}"
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get "$NXF_BASE/$version/nextflow?$action" "$tmpfile" "$1" || exit $?
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mv "$tmpfile" "$1" || exit $?
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chmod +rx "$1" || exit $?
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bash "$1" -download || exit $?
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echo ''
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echo -e $'Nextflow installation completed. Please note:'
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echo -e $'- the executable file `nextflow` has been created in the folder:' $(dirname $1)
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if [[ ! "$PATH" =~ (^|:)"$(dirname $1)"(:|$) ]]; then
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echo -e $'- you may complete the installation by moving it to a directory in your $PATH'
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fi
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echo ''
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}
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function check_latest() {
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[[ $cmd != run ]] && return 0
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[[ $NXF_OFFLINE == true || $NXF_DISABLE_CHECK_LATEST == true ]] && return 0
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local latest=$(get_ver "$NXF_BASE/$(current_ver)/version?current=$NXF_VER")
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if [[ -n "$latest" && $(cmp_ver "$latest" "$NXF_VER") -gt 0 ]]; then
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echo_yellow "Nextflow $latest is available - Please consider updating your version to it"
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fi
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}
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function launch_nextflow() {
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# the launch command line
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local cmdline=()
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# remove leading and trailing double-quotes
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for x in "${launcher[@]}"; do
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x="${x%\"}"
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x="${x#\"}"
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cmdline+=("$x")
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done
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if [[ "$bg" ]]; then
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local pid_file="${NXF_PID_FILE:-.nextflow.pid}"
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cmdline+=("${args[@]}")
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exec "${cmdline[@]}" &
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disown
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echo $! > "$pid_file"
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exit 0
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fi
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cmdline+=("${args[@]}")
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exec "${cmdline[@]}"
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exit 1
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}
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# check self-install
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if [ "$0" = "bash" ] || [[ "$0" =~ .*/bash ]]; then
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if [ -d nextflow ]; then
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echo 'Please note:'
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echo "- The install procedure needs to create a file named 'nextflow' in this folder, but a directory with this name already exists."
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echo "- Please renamed/delete that directory, or execute the Nextflow install procedure in another folder."
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echo ''
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exit 1
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fi
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install "$PWD/nextflow" install
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exit 0
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fi
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# clean up env
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# see https://github.com/nextflow-io/nextflow/issues/1716
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unset JAVA_TOOL_OPTIONS
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# parse the command line
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bg=''
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declare -a jvmopts=()
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declare -a args=("$@")
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declare -a commands=(clone config drop help history info ls pull run view node console kuberun)
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# $NXF_CLI_OPTS allow to pass arbitrary cli opts via the environment
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# note: do not wrap with quotes because the variable can be used to specify more than on option separate by blanks
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[ "$NXF_CLI_OPTS" ] && args+=($NXF_CLI_OPTS)
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cmd=''
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while [[ $# != 0 ]]; do
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case $1 in
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-D*)
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if [[ ! "$cmd" ]]; then
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jvmopts+=("$1")
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fi
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;;
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-bg)
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bg=1
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;;
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-remote-debug)
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echo_yellow "Enabling script debugging - continue the execution launching the remote VM debugger in your favourite IDE using port $NXF_REMOTE_DEBUG_PORT"
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remote_debug=1
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;;
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-download)
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if [[ ! "$cmd" ]]; then
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rm -rf "$NXF_DIST/$NXF_VER" || exit $?
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bash "$0" -version || exit $?
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exit 0
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fi
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;;
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-self-update|self-update)
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if [[ ! "$cmd" ]]; then
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[[ -z $NXF_EDGE && $NXF_VER = *-edge ]] && NXF_EDGE=1
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unset NXF_VER
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install "$0" update
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exit 0
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fi
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;;
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*)
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[[ $1 && $1 != -* && ! "$cmd" && ${commands[*]} =~ $1 ]] && cmd=$1
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;;
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esac
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shift
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done
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CAPSULE_LOG=${CAPSULE_LOG:=''}
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CAPSULE_RESET=${CAPSULE_RESET:=''}
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CAPSULE_CACHE_DIR=${CAPSULE_CACHE_DIR:="$NXF_HOME/capsule"}
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NXF_PACK=one
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NXF_MODE=${NXF_MODE:-''}
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NXF_JAR=${NXF_JAR:-nextflow-$NXF_VER-$NXF_PACK.jar}
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NXF_BIN=${NXF_BIN:-$NXF_DIST/$NXF_VER/$NXF_JAR}
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NXF_PATH=$(dirname "$NXF_BIN")
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NXF_URL=${NXF_URL:-$NXF_BASE/v$NXF_VER/$NXF_JAR}
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NXF_HOST=${HOSTNAME:-localhost}
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[[ $NXF_LAUNCHER ]] || NXF_LAUNCHER=${NXF_HOME}/tmp/launcher/nextflow-${NXF_PACK}_${NXF_VER}/${NXF_HOST}
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# both NXF_GRAB and NXF_CLASSPATH are not supported any more as of version 24.04.7-edge
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NXF_GRAB=${NXF_GRAB:-''}
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NXF_CLASSPATH=${NXF_CLASSPATH:-''}
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# Determine the path to this file
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if [[ $NXF_PACK = dist ]]; then
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NXF_BIN=$(which "$0" 2>/dev/null)
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[ $? -gt 0 -a -f "$0" ] && NXF_BIN="./$0"
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fi
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# use nextflow custom java home path
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if [[ "$NXF_JAVA_HOME" ]]; then
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JAVA_HOME="$NXF_JAVA_HOME"
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unset JAVA_CMD
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fi
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# Determine the Java command to use to start the JVM.
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if [ ! -x "$JAVA_CMD" ] ; then
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if [ -d "$JAVA_HOME" ] ; then
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if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
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# IBM's JDK on AIX uses strange locations for the executables
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JAVA_CMD="$JAVA_HOME/jre/sh/java"
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else
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JAVA_CMD="$JAVA_HOME/bin/java"
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fi
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elif [ -x /usr/libexec/java_home ]; then
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JAVA_CMD="$(/usr/libexec/java_home -v 17+ 2>/dev/null)/bin/java" || JAVA_CMD=java
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else
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JAVA_CMD="$(which java)" || JAVA_CMD=java
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fi
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fi
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# Retrieve the java version from a NF local file
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JAVA_KEY="$NXF_HOME/tmp/ver/$(resolve_link "$JAVA_CMD" | sed 's@/@.@g')"
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if [ -f "$JAVA_KEY" ]; then
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JAVA_VER="$(cat "$JAVA_KEY")"
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else
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JAVA_VER="$("$JAVA_CMD" $NXF_OPTS -version 2>&1)"
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if [ $? -ne 0 ]; then
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getstarted_web="https://www.nextflow.io/docs/latest/getstarted.html"
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echo_red "${JAVA_VER:-Failed to launch the Java virtual machine}"
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echo_red "NOTE: Nextflow needs a Java virtual machine to run. To this end:
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- make sure a \`java\` command can be found; or
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- manually define the variables JAVA_HOME to point to an existing installation; or
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- install a Java virtual machine, for instance through https://sdkman.io (read the docs);
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- for more details please refer to the Nextflow Get Started page at http://docs.nextflow.io."
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echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n NXF_OPTS: $NXF_OPTS\n"
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exit 1
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fi
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JAVA_VER=$(echo "$JAVA_VER" | awk '/version/ {gsub(/"/, "", $3); print $3}')
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# check NF version
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if [[ ! $NXF_VER =~ ([0-9]+)\.([0-9]+)\.([0-9].*) ]]; then
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echo_red "Not a valid Nextflow version: $NXF_VER"
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exit 1
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fi
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major=${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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version_message="Java 17 or later (up to 26)"
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if [[ ! $JAVA_VER =~ $version_check ]]; then
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echo_red "ERROR: Cannot find Java or it's a wrong version -- please make sure that $version_message is installed"
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if [[ "$NXF_JAVA_HOME" ]]; then
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echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n NXF_JAVA_HOME: $NXF_JAVA_HOME\n"
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else
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echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n JAVA_HOME: $JAVA_HOME\n"
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fi
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exit 1
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fi
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mkdir -p "$(dirname "$JAVA_KEY")"
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[[ -f $JAVA_VER ]] && echo $JAVA_VER > "$JAVA_KEY"
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fi
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# Verify nextflow jar is available
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if [ ! -f "$NXF_BIN" ]; then
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[ -f "$NXF_PATH" ] && rm "$NXF_PATH"
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mkdir -p "$NXF_PATH" || exit $?
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tmpfile=$(make_temp)
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get "$NXF_URL" "$tmpfile" "$NXF_BIN"
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mv "$tmpfile" "$NXF_BIN"
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fi
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COLUMNS=${COLUMNS:-`tty -s && tput cols 2>/dev/null || true`}
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declare -a JAVA_OPTS=()
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JAVA_OPTS+=(-Dfile.encoding=UTF-8 -Dcapsule.trampoline -Dcapsule.java.cmd="$JAVA_CMD" -Dcom.sun.security.enableAIAcaIssuers=true)
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if [[ $cmd == console ]]; then bg=1;
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else JAVA_OPTS+=(-Djava.awt.headless=true)
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fi
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if [[ $NXF_LEGACY_LAUNCHER ]]; then
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[[ "$JAVA_HOME" ]] && JAVA_OPTS+=(-Dcapsule.java.home="$JAVA_HOME")
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[[ "$CAPSULE_LOG" ]] && JAVA_OPTS+=(-Dcapsule.log=$CAPSULE_LOG)
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[[ "$CAPSULE_RESET" ]] && JAVA_OPTS+=(-Dcapsule.reset=true)
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fi
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[[ "$cmd" != "run" && "$cmd" != "node" ]] && JAVA_OPTS+=(-XX:+TieredCompilation -XX:TieredStopAtLevel=1)
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[[ "$NXF_OPTS" ]] && JAVA_OPTS+=($NXF_OPTS)
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[[ "$NXF_CLASSPATH" ]] && export NXF_CLASSPATH
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[[ "$NXF_GRAB" ]] && export NXF_GRAB
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[[ "$COLUMNS" ]] && export COLUMNS
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[[ "$NXF_TEMP" ]] && JAVA_OPTS+=(-Djava.io.tmpdir="$NXF_TEMP")
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[[ "${jvmopts[@]}" ]] && JAVA_OPTS+=("${jvmopts[@]}")
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export JAVA_CMD
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export CAPSULE_CACHE_DIR
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export NXF_PLUGINS_DIR
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export NXF_PLUGINS_MODE
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export NXF_PLUGINS_DEFAULT
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export NXF_PACK
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export NXF_ENABLE_VIRTUAL_THREADS
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# lookup the a `md5` command
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if hash md5sum 2>/dev/null; then MD5=md5sum;
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elif hash gmd5sum 2>/dev/null; then MD5=gmd5sum;
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elif hash md5 2>/dev/null; then MD5=md5;
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else MD5=''
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fi
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# when no md5 command is available fallback on default execution
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if [ ! "$MD5" ] || [ "$CAPSULE_RESET" ]; then
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launcher=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN"))
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launch_nextflow
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exit 1
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fi
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# creates a md5 unique for the given variables
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env_md5() {
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cat <<EOF | $MD5 | cut -f1 -d' '
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$JAVA_CMD
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$JAVA_VER
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${JAVA_OPTS[@]}
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$NXF_HOME
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$NXF_VER
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$NXF_OPTS
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$NXF_GRAB
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$NXF_CLASSPATH
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$NXF_JVM_ARGS
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$NXF_ENABLE_VIRTUAL_THREADS
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EOF
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}
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# checked if a cached classpath file exists and it newer that the nextflow boot jar file
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LAUNCH_FILE="${NXF_LAUNCHER}/classpath-$(env_md5)"
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if [ -s "$LAUNCH_FILE" ] && [ "$LAUNCH_FILE" -nt "$NXF_BIN" ] && [[ "$remote_debug" -ne 1 ]]; then
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declare -a launcher="($(cat "$LAUNCH_FILE"))"
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else
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if [[ $NXF_LEGACY_LAUNCHER ]]; then
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# otherwise run the capsule and get the result classpath in the 'launcher' and save it to a file
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cli=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN"))
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[[ $? -ne 0 ]] && echo_red 'Unable to initialize nextflow environment' && exit 1
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else
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# otherwise parse the command and get the result classpath in the 'launcher' and save it to a file
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cli=("\"$JAVA_CMD\"" "${JAVA_OPTS[@]}" -jar "$NXF_BIN")
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|
fi
|
|
|
|
# first string between double quotes is the full path to java, also blank spaces are included
|
|
# remainder string are arguments
|
|
# we extract first part into `cmd_base`` and remainder into `cmd_tail`` and convert them to array as previous version
|
|
cmd_pattern='"([^"]*)"(.*)'
|
|
[[ "${cli[@]}" =~ $cmd_pattern ]]
|
|
declare -a cmd_base="(${BASH_REMATCH[1]})"
|
|
declare -a cmd_tail="(${BASH_REMATCH[2]})"
|
|
|
|
launcher="${cmd_base[@]}"
|
|
[[ "$NXF_JVM_ARGS" ]] && launcher+=($NXF_JVM_ARGS)
|
|
[[ "$remote_debug" ]] && launcher+=(-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=$NXF_REMOTE_DEBUG_PORT)
|
|
|
|
launcher+=(--add-opens=java.base/java.lang=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/java.io=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/java.nio=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/java.net=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/java.util=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/sun.nio.ch=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/sun.nio.fs=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/jdk.internal.vm=ALL-UNNAMED)
|
|
launcher+=(--add-opens=java.base/java.util.regex=ALL-UNNAMED)
|
|
if [[ "$JAVA_VER" =~ ^(24|25|26) ]]; then
|
|
launcher+=(--enable-native-access=ALL-UNNAMED)
|
|
launcher+=(--sun-misc-unsafe-memory-access=allow)
|
|
fi
|
|
if [[ "$NXF_ENABLE_VIRTUAL_THREADS" == 'true' ]]; then
|
|
if [[ "$JAVA_VER" =~ ^(19|20) ]]; then launcher+=(--enable-preview)
|
|
elif [[ ! "$JAVA_VER" =~ ^(21|22|23|24|25|26) ]]; then die "Virtual threads require Java 19 or later - current version $JAVA_VER"
|
|
fi
|
|
fi
|
|
launcher+=("${cmd_tail[@]}")
|
|
|
|
# create the launch file only when using the legacy launcher (capsule)
|
|
if [[ $NXF_LEGACY_LAUNCHER ]]; then
|
|
# Don't show errors if the LAUNCH_FILE can't be created
|
|
if mkdir -p "${NXF_LAUNCHER}" 2>/dev/null; then
|
|
STR=''
|
|
for x in "${launcher[@]}"; do
|
|
[[ "$x" != "\"-Duser.dir=$PWD\"" ]] && [[ ! "$x" == *"-agentlib:jdwp"* ]] && STR+=$(printf '%q ' "$x")
|
|
done
|
|
printf "$STR">"$LAUNCH_FILE"
|
|
else
|
|
echo_yellow "Warning: Couldn't create cached classpath folder: $NXF_LAUNCHER -- Maybe NXF_HOME is not writable?"
|
|
fi
|
|
fi
|
|
|
|
fi
|
|
|
|
# check for latest version
|
|
check_latest
|
|
# finally run it
|
|
launch_nextflow
|