mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
Removed nextflow file
This commit is contained in:
sruthipsuresh
sruthipsuresh
parent
4fca435120
commit
4ada27479a
1 changed files with 0 additions and 470 deletions
470
nextflow
470
nextflow
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@ -1,470 +0,0 @@
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#!/usr/bin/env bash
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#
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# Copyright 2020, Seqera Labs
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# Copyright 2013-2019, Centre for Genomic Regulation (CRG)
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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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[[ "$NXF_DEBUG" == 'x' ]] && set -x
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NXF_VER=${NXF_VER:-'20.10.0'}
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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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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 -q '$1' -O '$2'"
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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:-$2}"
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echo ""
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exit 1
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fi
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}
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function make_temp() {
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local base=${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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[[ $NXF_EDGE == 1 ]] && printf 'edge' || printf 'latest'
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}
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function install() {
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local tmpfile=$(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 +x "$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 $PATH'
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fi
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echo ''
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}
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function launch_nextflow() {
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# the launch command line
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local cmdline=()
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# remove leading and trailing double-quotes
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for x in "${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 [[ $NXF_MPIRUN ]]; then
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local rank=''
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[[ $SLURM_PROCID ]] && rank=$SLURM_PROCID
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[[ $OMPI_COMM_WORLD_RANK ]] && rank=$OMPI_COMM_WORLD_RANK
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if [[ ! $rank ]]; then
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echo_red 'It looks you are not running in a MPI enabled environment -- cannot find `$OMPI_COMM_WORLD_RANK` nor `$SLURM_PROCID` variable';
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exit 1;
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fi
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if [[ $SLURM_CPUS_PER_TASK && $SLURM_MEM_PER_CPU ]]; then
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export NXF_CLUSTER_MAXCPUS=$SLURM_CPUS_PER_TASK
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export NXF_CLUSTER_MAXMEMORY="$(($SLURM_MEM_PER_CPU*$SLURM_CPUS_PER_TASK))MB"
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fi
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if [[ $rank == 0 ]]; then
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# sleep a few seconds in order to wait worker daemons to bootstrap
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sleep ${NXF_SLEEP:-10}
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export NXF_EXECUTOR='ignite'
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export NXF_CLUSTER_SHUTDOWNONCOMPLETE='true'
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else
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args=(-log .nextflow_node_${rank}.log node ignite)
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fi
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# start in daemon mode
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elif [[ "$bg" ]]; then
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local pid_file="${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" ] || [ "$0" = "/bin/bash" ]; then
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if [ -d nextflow ]; then
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echo 'Please note:'
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echo "- The install procedure needs to create a file named 'nextflow' in this folder, but a directory with this name already exists."
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echo "- Please renamed/delete that directory, or execute the Nextflow install procedure in another folder."
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echo ''
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exit 1
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fi
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install "$PWD/nextflow" install
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exit 0
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fi
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# parse the command line
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bg=''
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dockerize=''
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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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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+=("$1")
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fi
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;;
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-d|-dockerize)
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if [[ ! "$cmd" && ! -f /.nextflow/dockerized ]]; then
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dockerize=1
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fi
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;;
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-bg)
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if [[ ! -f /.nextflow/dockerized ]]; then
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bg=1
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fi
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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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-process.executor|-executor.name)
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if [[ $2 && $2 == 'ignite' ]]; then
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[ ! $NXF_MODE ] && NXF_MODE='ignite'; shift;
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fi
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;;
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-with-mpi)
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[ ! $NXF_MODE ] && NXF_MODE='ignite'
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NXF_MPIRUN='true'
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;;
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*)
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[[ $1 && $1 != -* && ! "$cmd" && ${commands[*]} =~ $1 ]] && cmd=$1
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;;
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esac
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shift
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done
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NXF_DOCKER_OPTS=${NXF_DOCKER_OPTS:=''}
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if [[ "$dockerize" ]]; then
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if [[ "$bg" ]]; then detach='--detach '; else detach=''; fi
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NXF_ASSETS=${NXF_ASSETS:-${NXF_HOME:-$HOME/.nextflow}/assets}
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mkdir -p "$NXF_ASSETS"
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exec docker run $detach --rm --net host \
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-e NXF_ANSI_LOG=false \
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-e USER -e HOME -e NXF_ASSETS=$NXF_ASSETS -e NXF_USRMAP=$(id -u) -e NXF_DOCKER_OPTS='-u $(id -u)' \
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-v /var/run/docker.sock:/var/run/docker.sock \
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-v $HOME:$HOME:ro,Z -v $NXF_ASSETS:$NXF_ASSETS:Z -v $PWD:$PWD:Z -w $PWD $NXF_DOCKER_OPTS \
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nextflow/nextflow:$NXF_VER nextflow "${args[@]}"
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exit 1
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fi
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CAPSULE_LOG=${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/$NXF_JAR}
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NXF_GRAB=${NXF_GRAB:-''}
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NXF_CLASSPATH=${NXF_CLASSPATH:-''}
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NXF_MPIRUN=${NXF_MPIRUN:=''}
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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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[ ! $NXF_MODE ] && [[ $NXF_CLOUD_DRIVER == google ]] && NXF_MODE='google'
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[ ! $NXF_MODE ] && [[ $GOOGLE_APPLICATION_CREDENTIALS ]] && NXF_MODE='google'
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if [[ $NXF_MODE == ignite ]]; then
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# Fix JDK bug when there's a limit on the OS virtual memory
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# https://bugs.openjdk.java.net/browse/JDK-8044054
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# https://issues.apache.org/jira/browse/HADOOP-7154
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export MALLOC_ARENA_MAX=4
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fi
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# Determine the path to this file
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if [[ $NXF_PACK = all ]]; then
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NXF_BIN=$(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="$(/usr/libexec/java_home -v 1.8+)/bin/java"
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else
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||||||
JAVA_CMD="$(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 [ $? -ne 0 ]; then
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echo_red "${JAVA_VER:-Failed to launch the Java virtual machine}"
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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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||||||
# legacy version - Java 7/8 only
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||||||
if [ $major -eq 0 ] && [ $minor -lt 26 ]; then
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||||||
version_check="^(1.7|1.8)"
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||||||
version_message="Java 7 or 8"
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||||||
else
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|
||||||
version_check="^(1.8|9|10|11|12|13|14|15)"
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|
||||||
version_message="Java 8 or later"
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|
||||||
fi
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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"
|
|
||||||
fi
|
|
||||||
exit 1
|
|
||||||
fi
|
|
||||||
if [[ ! $JAVA_VER =~ ^(1.8|9|10|11|12|13|14|15) ]]; then
|
|
||||||
echo_yellow "NOTE: Nextflow is not tested with Java $JAVA_VER -- It's recommended the use of version 8 up to 15\n"
|
|
||||||
elif [[ ! $JAVA_VER =~ ^(1.8|9|10|11) && $NXF_MODE == ignite ]]; then
|
|
||||||
echo_yellow "WARN: Apache Ignite executor is not tested with Java $JAVA_VER -- It's recommended the use of version 8 up to 11\n"
|
|
||||||
fi
|
|
||||||
mkdir -p $(dirname "$JAVA_KEY")
|
|
||||||
[[ -f $JAVA_VER ]] && echo $JAVA_VER > "$JAVA_KEY"
|
|
||||||
fi
|
|
||||||
|
|
||||||
# Verify nextflow jar is available
|
|
||||||
if [ ! -f "$NXF_BIN" ]; then
|
|
||||||
[ -f "$NXF_PATH" ] && rm "$NXF_PATH"
|
|
||||||
mkdir -p "$NXF_PATH" || exit $?
|
|
||||||
tmpfile=$(make_temp)
|
|
||||||
get "$NXF_URL" "$tmpfile" "$NXF_BIN"
|
|
||||||
mv "$tmpfile" "$NXF_BIN"
|
|
||||||
fi
|
|
||||||
|
|
||||||
[[ "$cmd" == "console" ]] && NXF_MODE='console'
|
|
||||||
[[ "$cmd" == "node" && ! "$NXF_MODE" ]] && NXF_MODE='ignite'
|
|
||||||
|
|
||||||
COLUMNS=${COLUMNS:-`tty -s && tput cols 2>/dev/null || true`}
|
|
||||||
declare -a JAVA_OPTS=()
|
|
||||||
JAVA_OPTS+=(-Dfile.encoding=UTF-8 -Dcapsule.trampoline -Dcapsule.java.cmd="$JAVA_CMD")
|
|
||||||
if [[ $cmd == console ]]; then bg=1;
|
|
||||||
else JAVA_OPTS+=(-Djava.awt.headless=true)
|
|
||||||
fi
|
|
||||||
|
|
||||||
[[ "$NXF_MODE" ]] && JAVA_OPTS+=(-Dcapsule.mode=$NXF_MODE)
|
|
||||||
[[ "$JAVA_HOME" ]] && JAVA_OPTS+=(-Dcapsule.java.home="$JAVA_HOME")
|
|
||||||
[[ "$CAPSULE_LOG" ]] && JAVA_OPTS+=(-Dcapsule.log=$CAPSULE_LOG)
|
|
||||||
[[ "$CAPSULE_RESET" ]] && JAVA_OPTS+=(-Dcapsule.reset=true)
|
|
||||||
[[ "$cmd" != "run" && "$cmd" != "node" ]] && JAVA_OPTS+=(-XX:+TieredCompilation -XX:TieredStopAtLevel=1)
|
|
||||||
[[ "$NXF_OPTS" ]] && JAVA_OPTS+=($NXF_OPTS)
|
|
||||||
[[ "$NXF_CLASSPATH" ]] && export NXF_CLASSPATH
|
|
||||||
[[ "$NXF_GRAB" ]] && export NXF_GRAB
|
|
||||||
[[ "$COLUMNS" ]] && export COLUMNS
|
|
||||||
[[ "$NXF_TEMP" ]] && JAVA_OPTS+=(-Djava.io.tmpdir="$NXF_TEMP")
|
|
||||||
[[ "${jvmopts[@]}" ]] && JAVA_OPTS+=("${jvmopts[@]}")
|
|
||||||
# use drip to speedup startup time -- https://github.com/ninjudd/drip
|
|
||||||
[[ "$NXF_DRIP" ]] && export DRIP_INIT='' && export DRIP_INIT_CLASS='nextflow.cli.DripMain'
|
|
||||||
export JAVA_CMD
|
|
||||||
export CAPSULE_CACHE_DIR
|
|
||||||
|
|
||||||
# lookup the a `md5` command
|
|
||||||
if hash md5sum 2>/dev/null; then MD5=md5sum;
|
|
||||||
elif hash gmd5sum 2>/dev/null; then MD5=gmd5sum;
|
|
||||||
elif hash md5 2>/dev/null; then MD5=md5;
|
|
||||||
else MD5=''
|
|
||||||
fi
|
|
||||||
|
|
||||||
# when no md5 command is available fallback on default execution
|
|
||||||
if [ ! "$MD5" ] || [ "$CAPSULE_RESET" ]; then
|
|
||||||
launcher=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN"))
|
|
||||||
launch_nextflow
|
|
||||||
exit 1
|
|
||||||
fi
|
|
||||||
|
|
||||||
# creates a md5 unique for the given variables
|
|
||||||
env_md5() {
|
|
||||||
cat <<EOF | $MD5 | cut -f1 -d' '
|
|
||||||
$JAVA_CMD
|
|
||||||
$JAVA_VER
|
|
||||||
${JAVA_OPTS[@]}
|
|
||||||
$NXF_HOME
|
|
||||||
$NXF_VER
|
|
||||||
$NXF_OPTS
|
|
||||||
$NXF_GRAB
|
|
||||||
$NXF_CLASSPATH
|
|
||||||
$NXF_DRIP
|
|
||||||
EOF
|
|
||||||
}
|
|
||||||
|
|
||||||
# checked if a cached classpath file exists and it newer that the nextflow boot jar file
|
|
||||||
if [[ -f /.nextflow/dockerized ]]; then
|
|
||||||
LAUNCH_FILE=/.nextflow/launch-classpath
|
|
||||||
else
|
|
||||||
LAUNCH_FILE="${NXF_LAUNCHER}/classpath-$(env_md5)"
|
|
||||||
fi
|
|
||||||
if [ -s "$LAUNCH_FILE" ] && [ "$LAUNCH_FILE" -nt "$NXF_BIN" ]; then
|
|
||||||
launcher=($(cat "$LAUNCH_FILE"))
|
|
||||||
else
|
|
||||||
# otherwise run the capsule and get the result classpath in the 'launcher' and save it to a file
|
|
||||||
cli=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN"))
|
|
||||||
[[ $? -ne 0 ]] && echo_red 'Unable to initialize nextflow environment' && exit 1
|
|
||||||
|
|
||||||
if [[ "$JAVA_VER" =~ ^(9|10|11|12|13|14|15) ]]; then
|
|
||||||
launcher=("${cli[@]:0:1}")
|
|
||||||
launcher+=(--add-opens=java.base/java.lang=ALL-UNNAMED)
|
|
||||||
launcher+=(--add-opens=java.base/java.io=ALL-UNNAMED)
|
|
||||||
launcher+=(--add-opens=java.base/java.nio=ALL-UNNAMED)
|
|
||||||
launcher+=(--add-opens=java.base/java.util=ALL-UNNAMED)
|
|
||||||
launcher+=(--add-opens=java.base/sun.nio.ch=ALL-UNNAMED)
|
|
||||||
launcher+=(--add-opens=java.base/sun.nio.fs=ALL-UNNAMED)
|
|
||||||
launcher+=(--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED)
|
|
||||||
launcher+=(--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED)
|
|
||||||
launcher+=(--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED)
|
|
||||||
launcher+=(--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED)
|
|
||||||
launcher+=(--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED)
|
|
||||||
launcher+=(--illegal-access=deny)
|
|
||||||
launcher+=("${cli[@]:1}")
|
|
||||||
else
|
|
||||||
launcher=("${cli[@]}")
|
|
||||||
fi
|
|
||||||
|
|
||||||
# Don't show errors if the LAUNCH_FILE can't be created
|
|
||||||
if mkdir -p "${NXF_LAUNCHER}" 2>/dev/null; then
|
|
||||||
STR=''
|
|
||||||
for x in "${launcher[@]}"; do
|
|
||||||
[[ "$x" != "\"-Duser.dir=$PWD\"" ]] && STR+="$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
|
|
||||||
|
|
||||||
# finally run it
|
|
||||||
launch_nextflow
|
|
||||||
Loading…
Reference in a new issue