From 4ada27479a856515a769dbfd6d3d8f63631052b6 Mon Sep 17 00:00:00 2001 From: sruthipsuresh <58604926+sruthipsuresh@users.noreply.github.com> Date: Mon, 21 Dec 2020 09:36:32 -0600 Subject: [PATCH] Removed nextflow file --- nextflow | 470 ------------------------------------------------------- 1 file changed, 470 deletions(-) delete mode 100755 nextflow diff --git a/nextflow b/nextflow deleted file mode 100755 index 44392ce8..00000000 --- a/nextflow +++ /dev/null @@ -1,470 +0,0 @@ -#!/usr/bin/env bash -# -# Copyright 2020, Seqera Labs -# Copyright 2013-2019, Centre for Genomic Regulation (CRG) -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -[[ "$NXF_DEBUG" == 'x' ]] && set -x -NXF_VER=${NXF_VER:-'20.10.0'} -NXF_ORG=${NXF_ORG:-'nextflow-io'} -NXF_HOME=${NXF_HOME:-$HOME/.nextflow} -NXF_PROT=${NXF_PROT:-'https'} -NXF_BASE=${NXF_BASE:-$NXF_PROT://www.nextflow.io/releases} -NXF_TEMP=${NXF_TEMP:-$TMPDIR} -NXF_DIST=${NXF_DIST:-$NXF_HOME/framework} -NXF_CLI="$0 $@" - -export NXF_CLI -export NXF_ORG -export NXF_HOME - -if [[ $TERM && $TERM != 'dumb' ]]; then -if command -v tput &>/dev/null; then -GREEN=$(tput setaf 2; tput bold) -YELLOW=$(tput setaf 3) -RED=$(tput setaf 1) -NORMAL=$(tput sgr0) -fi -fi - -function echo_red() { - >&2 echo -e "$RED$*$NORMAL" -} - -function echo_green() { - echo -e "$GREEN$*$NORMAL" -} - -function echo_yellow() { - >&2 echo -e "$YELLOW$*$NORMAL" -} - -function die() { - echo_red "$*" - exit 1 -} - -function get_abs_filename() { - echo "$(cd "$(dirname "$1")" && pwd)/$(basename "$1")" -} - -function get() { - if command -v curl &>/dev/null; then - GET="curl -fsSL '$1' -o '$2'" - elif command -v wget &>/dev/null; then - GET="wget -q '$1' -O '$2'" - else - echo_red "ERROR: Cannot find 'curl' nor 'wget' utility -- please install one of them" - exit 1 - fi - - printf "Downloading nextflow dependencies. It may require a few seconds, please wait .. " - eval $GET; status=$? - printf "\r\033[K" - if [ $status -ne 0 ]; then - echo_red "ERROR: Cannot download nextflow required file -- make sure you can connect to the internet" - echo "" - echo "Alternatively you can try to download this file:" - echo " $1" - echo "" - echo "and save it as:" - echo " ${3:-$2}" - echo "" - exit 1 - fi -} - -function make_temp() { - local base=${NXF_TEMP:=$PWD} - if [ "$(uname)" = 'Darwin' ]; then mktemp "${base}/nxf-tmp.XXXXXX" || exit $? - else mktemp -t nxf-tmp.XXXXXX -p "${base}" || exit $? - fi -} - -function resolve_link() { - [[ ! -f $1 ]] && exit 1 - if command -v realpath &>/dev/null; then - realpath "$1" - elif command -v readlink &>/dev/null; then - local target="$1" - cd $(dirname $target); target=$(basename $target) - while [ -L "$target" ]; do - target="$(readlink "$target")" - cd $(dirname $target); target=$(basename $target) - done - echo "$(cd "$(dirname "$target")"; pwd -P)/$target" - else - echo_yellow "WARN: Neither \`realpath\` nor \`readlink\` command can be found" - exit 1 - fi -} - -function current_ver() { - [[ $NXF_EDGE == 1 ]] && printf 'edge' || printf 'latest' -} - -function install() { - local tmpfile=$(make_temp) - local version=$(set +u; [[ $NXF_VER ]] && printf "v$NXF_VER" || current_ver) - local action="a=${2:-default}" - get "$NXF_BASE/$version/nextflow?$action" "$tmpfile" "$1" || exit $? - mv "$tmpfile" "$1" || exit $? - chmod +x "$1" || exit $? - bash "$1" -download || exit $? - echo '' - echo -e $'Nextflow installation completed. Please note:' - echo -e $'- the executable file `nextflow` has been created in the folder:' $(dirname $1) - if [[ ! "$PATH" =~ (^|:)"$(dirname $1)"(:|$) ]]; then - echo -e $'- you may complete the installation by moving it to a directory in your $PATH' - fi - echo '' -} - -function launch_nextflow() { - # the launch command line - local cmdline=() - # remove leading and trailing double-quotes - for x in "${launcher[@]}"; do - x="${x%\"}" - x="${x#\"}" - cmdline+=("$x") - done - - if [[ $NXF_MPIRUN ]]; then - local rank='' - [[ $SLURM_PROCID ]] && rank=$SLURM_PROCID - [[ $OMPI_COMM_WORLD_RANK ]] && rank=$OMPI_COMM_WORLD_RANK - if [[ ! $rank ]]; then - echo_red 'It looks you are not running in a MPI enabled environment -- cannot find `$OMPI_COMM_WORLD_RANK` nor `$SLURM_PROCID` variable'; - exit 1; - fi - if [[ $SLURM_CPUS_PER_TASK && $SLURM_MEM_PER_CPU ]]; then - export NXF_CLUSTER_MAXCPUS=$SLURM_CPUS_PER_TASK - export NXF_CLUSTER_MAXMEMORY="$(($SLURM_MEM_PER_CPU*$SLURM_CPUS_PER_TASK))MB" - fi - if [[ $rank == 0 ]]; then - # sleep a few seconds in order to wait worker daemons to bootstrap - sleep ${NXF_SLEEP:-10} - export NXF_EXECUTOR='ignite' - export NXF_CLUSTER_SHUTDOWNONCOMPLETE='true' - else - args=(-log .nextflow_node_${rank}.log node ignite) - fi - # start in daemon mode - elif [[ "$bg" ]]; then - local pid_file="${NXF_PID_FILE:-.nextflow.pid}" - cmdline+=("${args[@]}") - exec "${cmdline[@]}" & - disown - echo $! > "$pid_file" - exit 0 - fi - - cmdline+=("${args[@]}") - exec "${cmdline[@]}" - exit 1 -} - -# check self-install -if [ "$0" = "bash" ] || [ "$0" = "/bin/bash" ]; then - if [ -d nextflow ]; then - echo 'Please note:' - echo "- The install procedure needs to create a file named 'nextflow' in this folder, but a directory with this name already exists." - echo "- Please renamed/delete that directory, or execute the Nextflow install procedure in another folder." - echo '' - exit 1 - fi - install "$PWD/nextflow" install - exit 0 -fi - - -# parse the command line -bg='' -dockerize='' -declare -a jvmopts=() -declare -a args=("$@") -declare -a commands=(clone config drop help history info ls pull run view node console kuberun) -cmd='' -while [[ $# != 0 ]]; do - case $1 in - -D*) - if [[ ! "$cmd" ]]; then - jvmopts+=("$1") - fi - ;; - -d|-dockerize) - if [[ ! "$cmd" && ! -f /.nextflow/dockerized ]]; then - dockerize=1 - fi - ;; - -bg) - if [[ ! -f /.nextflow/dockerized ]]; then - bg=1 - fi - ;; - -download) - if [[ ! "$cmd" ]]; then - rm -rf "$NXF_DIST/$NXF_VER" || exit $? - bash "$0" -version || exit $? - exit 0 - fi - ;; - -self-update|self-update) - if [[ ! "$cmd" ]]; then - [[ -z $NXF_EDGE && $NXF_VER = *-edge ]] && NXF_EDGE=1 - unset NXF_VER - install "$0" update - exit 0 - fi - ;; - -process.executor|-executor.name) - if [[ $2 && $2 == 'ignite' ]]; then - [ ! $NXF_MODE ] && NXF_MODE='ignite'; shift; - fi - ;; - -with-mpi) - [ ! $NXF_MODE ] && NXF_MODE='ignite' - NXF_MPIRUN='true' - ;; - *) - [[ $1 && $1 != -* && ! "$cmd" && ${commands[*]} =~ $1 ]] && cmd=$1 - ;; - esac - shift -done - -NXF_DOCKER_OPTS=${NXF_DOCKER_OPTS:=''} -if [[ "$dockerize" ]]; then - if [[ "$bg" ]]; then detach='--detach '; else detach=''; fi - NXF_ASSETS=${NXF_ASSETS:-${NXF_HOME:-$HOME/.nextflow}/assets} - mkdir -p "$NXF_ASSETS" - exec docker run $detach --rm --net host \ - -e NXF_ANSI_LOG=false \ - -e USER -e HOME -e NXF_ASSETS=$NXF_ASSETS -e NXF_USRMAP=$(id -u) -e NXF_DOCKER_OPTS='-u $(id -u)' \ - -v /var/run/docker.sock:/var/run/docker.sock \ - -v $HOME:$HOME:ro,Z -v $NXF_ASSETS:$NXF_ASSETS:Z -v $PWD:$PWD:Z -w $PWD $NXF_DOCKER_OPTS \ - nextflow/nextflow:$NXF_VER nextflow "${args[@]}" - exit 1 -fi - -CAPSULE_LOG=${CAPSULE_LOG:=''} -CAPSULE_RESET=${CAPSULE_RESET:=''} -CAPSULE_CACHE_DIR=${CAPSULE_CACHE_DIR:="$NXF_HOME/capsule"} - -NXF_PACK=one -NXF_MODE=${NXF_MODE:-''} -NXF_JAR=${NXF_JAR:-nextflow-$NXF_VER-$NXF_PACK.jar} -NXF_BIN=${NXF_BIN:-$NXF_DIST/$NXF_VER/$NXF_JAR} -NXF_PATH=$(dirname "$NXF_BIN") -NXF_URL=${NXF_URL:-$NXF_BASE/v$NXF_VER/$NXF_JAR} -NXF_GRAB=${NXF_GRAB:-''} -NXF_CLASSPATH=${NXF_CLASSPATH:-''} -NXF_MPIRUN=${NXF_MPIRUN:=''} -NXF_HOST=${HOSTNAME:-localhost} -[[ $NXF_LAUNCHER ]] || NXF_LAUNCHER=${NXF_HOME}/tmp/launcher/nextflow-${NXF_PACK}_${NXF_VER}/${NXF_HOST} - -[ ! $NXF_MODE ] && [[ $NXF_CLOUD_DRIVER == google ]] && NXF_MODE='google' -[ ! $NXF_MODE ] && [[ $GOOGLE_APPLICATION_CREDENTIALS ]] && NXF_MODE='google' - -if [[ $NXF_MODE == ignite ]]; then - # Fix JDK bug when there's a limit on the OS virtual memory - # https://bugs.openjdk.java.net/browse/JDK-8044054 - # https://issues.apache.org/jira/browse/HADOOP-7154 - export MALLOC_ARENA_MAX=4 -fi - -# Determine the path to this file -if [[ $NXF_PACK = all ]]; then - NXF_BIN=$(which "$0" 2>/dev/null) - [ $? -gt 0 -a -f "$0" ] && NXF_BIN="./$0" -fi - -# use nextflow custom java home path -if [[ "$NXF_JAVA_HOME" ]]; then - JAVA_HOME="$NXF_JAVA_HOME" - unset JAVA_CMD -fi -# Determine the Java command to use to start the JVM. -if [ ! -x "$JAVA_CMD" ] ; then - if [ -d "$JAVA_HOME" ] ; then - if [ -x "$JAVA_HOME/jre/sh/java" ] ; then - # IBM's JDK on AIX uses strange locations for the executables - JAVA_CMD="$JAVA_HOME/jre/sh/java" - else - JAVA_CMD="$JAVA_HOME/bin/java" - fi - elif [ -x /usr/libexec/java_home ]; then - JAVA_CMD="$(/usr/libexec/java_home -v 1.8+)/bin/java" - else - JAVA_CMD="$(which java)" || JAVA_CMD=java - fi -fi - -# Retrieve the java version from a NF local file -JAVA_KEY="$NXF_HOME/tmp/ver/$(resolve_link "$JAVA_CMD" | sed 's@/@.@g')" -if [ -f "$JAVA_KEY" ]; then - JAVA_VER="$(cat "$JAVA_KEY")" -else - JAVA_VER="$("$JAVA_CMD" $NXF_OPTS -version 2>&1)" - if [ $? -ne 0 ]; then - echo_red "${JAVA_VER:-Failed to launch the Java virtual machine}" - 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: $NXF_OPTS\n" - exit 1 - fi - JAVA_VER=$(echo "$JAVA_VER" | awk '/version/ {gsub(/"/, "", $3); print $3}') - # check NF version - if [[ ! $NXF_VER =~ ([0-9]+)\.([0-9]+)\.([0-9].*) ]]; then - echo_red "Not a valid Nextflow version: $NXF_VER" - exit 1 - fi - major=${BASH_REMATCH[1]} - minor=${BASH_REMATCH[2]} - # legacy version - Java 7/8 only - if [ $major -eq 0 ] && [ $minor -lt 26 ]; then - version_check="^(1.7|1.8)" - version_message="Java 7 or 8" - else - version_check="^(1.8|9|10|11|12|13|14|15)" - version_message="Java 8 or later" - fi - if [[ ! $JAVA_VER =~ $version_check ]]; then - echo_red "ERROR: Cannot find Java or it's a wrong version -- please make sure that $version_message is installed" - if [[ "$NXF_JAVA_HOME" ]]; then - 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" - else - 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 </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