nextflow

#!/usr/bin/env bash
#
#  Copyright 2020-2022, 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:-'22.10.7'}
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 $@"
NXF_CLI_OPTS=${NXF_CLI_OPTS:-}

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 [[ "$bg" ]]; then
      local pid_file="${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" ] || [[ "$0" =~ .*/bash ]]; then
    if [ -d nextflow ]; then
        echo 'Please note:'
        echo "- The install procedure needs to create a file named 'nextflow' in this folder, but a directory with this name already exists."
        echo "- Please renamed/delete that directory, or execute the Nextflow install procedure in another folder."
        echo ''
        exit 1
    fi
    install "$PWD/nextflow" install
    exit 0
fi

# clean up env
# see https://github.com/nextflow-io/nextflow/issues/1716
unset JAVA_TOOL_OPTIONS

# 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)
# $NXF_CLI_OPTS allow to pass arbitrary cli opts via the environment
# note: do not wrap with quotes because the variable can be used to specify more than on option separate by blanks
[ "$NXF_CLI_OPTS" ] && args+=($NXF_CLI_OPTS)

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
      ;;
    *)
      [[ $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_HOST=${HOSTNAME:-localhost}
[[ $NXF_LAUNCHER ]] || NXF_LAUNCHER=${NXF_HOME}/tmp/launcher/nextflow-${NXF_PACK}_${NXF_VER}/${NXF_HOST}

# 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|16|17|18)"
    version_message="Java 8 or later (up to 18)"
  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 =~ ^(11|12|13|14|15|16|17|18) ]]; then
      echo_yellow "NOTE: Nextflow is not tested with Java $JAVA_VER -- It's recommended the use of version 11 up to 18\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

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" -Dcom.sun.security.enableAIAcaIssuers=true)
if [[ $cmd == console ]]; then bg=1;
else JAVA_OPTS+=(-Djava.awt.headless=true)
fi

[[ "$JAVA_HOME" ]] && JAVA_OPTS+=(-Dcapsule.java.home="$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[@]}")
export JAVA_CMD
export CAPSULE_CACHE_DIR
export NXF_PLUGINS_DIR
export NXF_PLUGINS_MODE
export NXF_PLUGINS_DEFAULT
export NXF_PACK

# 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_JVM_ARGS
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 "$NXF_BIN" ]; then
    declare -a launcher="($(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

    # 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[@]}" =~ $cmd_pattern ]]
    cmd_base=(${BASH_REMATCH[1]})
    cmd_tail=(${BASH_REMATCH[2]})

    if [[ "$JAVA_VER" =~ ^(9|10|11|12|13|14|15|16|17|18) ]]; then
      launcher="${cmd_base[@]}"
      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)
      [[ "$NXF_JVM_ARGS" ]] && launcher+=($NXF_JVM_ARGS)
      launcher+=("${cmd_tail[@]}")
    else
      launcher="${cmd_base[@]}"
      [[ "$NXF_JVM_ARGS" ]] && launcher+=($NXF_JVM_ARGS)
      launcher+=("${cmd_tail[@]}")
    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