nextflow

#!/bin/bash
#
#  Copyright (c) 2013-2015, Centre for Genomic Regulation (CRG).
#  Copyright (c) 2013-2015, Paolo Di Tommaso and the respective authors.
#
#  This file is part of Nextflow.
#
#  Nextflow is free software: you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation, either version 3 of the License, or
#  (at your option) any later version.
#
#  Nextflow is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
#
#  You should have received a copy of the GNU General Public License
#  along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.

if [[ $TERM && $TERM != 'dumb' ]]; then
GREEN=$(tput setaf 2; tput bold)
YELLOW=$(tput setaf 3)
RED=$(tput setaf 1)
NORMAL=$(tput sgr0)
fi

function echo_red() {
    echo -e "$RED$*$NORMAL"
}

function echo_green() {
    echo -e "$GREEN$*$NORMAL"
}

function echo_yellow() {
    echo -e "$YELLOW$*$NORMAL"
}

function die() {
  echo_red "$*"
  exit 1
}

get_abs_filename() {
  echo "$(cd "$(dirname "$1")" && pwd)/$(basename "$1")"
}

function get() {
    if command -v wget &>/dev/null; then
        GET="wget -q $1 -O $2"
    elif command -v curl &>/dev/null; then
        GET="curl -fsSL $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 some seconds, please wait .. "
    $GET; status=$?
    printf "\r\033[K"
    if [ $status -ne 0 ]; then
        echo_red "Error: cannot download nextflow required file -- make sure you can connect the internet"
        echo ""
        echo "Alternatively you can download the file:"
        echo "    $1"
        echo ""
        echo "And save it as:"
        echo "    ${3:-$2}"
        echo ""
        exit 1
    fi
}

function install() {
    if [ "$(uname)" = 'Darwin' ]; then tmpfile=$(mktemp $PWD/XXXXX) || exit $?
    else tmpfile=$(mktemp -t XXXXX -p $PWD) || exit $?
    fi

    get "http://www.nextflow.io/releases/latest/nextflow" "$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)
    echo -e $'- you may complete the installation copying it to directory in your $PATH'
    echo ''
}

function launch_nextflow() {
    # the launch command line
    local cmdline="${launcher[@]} ${args[@]}"

    # start in daemon mode
    if [[ "$bg" ]]; then
      local pid_file="${NXF_PID_FILE:-.nextflow.pid}"
      bash -c "exec $cmdline" &
      disown
      printf $! > "$pid_file"
      exit 0
    fi
    # trampoline syntax -- https://github.com/puniverse/capsule/pull/71
    exec bash -c "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"
    exit 0
fi

NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
NXF_VER=${NXF_VER:-'0.15.6'}
NXF_ORG=${NXF_ORG:-'nextflow-io'}
NXF_ASSETS=${NXF_ASSETS:-$NXF_HOME/assets}
NXF_CLI="$0 $@"

export NXF_CLI
export NXF_ORG
export NXF_HOME

# Check if it is required to run in background
bg=''
declare -a jvmopts=()
declare -a args=("$@")
declare -a cli=(clone config drop help history info ls pull run view node console)
cmd=''
while [[ $# != 0 ]]; do
    case $1 in
    -D*)
      if [[ ! "$cmd" ]]; then
      jvmopts+=("$1")
      fi
      ;;
    -bg)
      bg=1
      ;;
    -download)
      if [[ ! "$cmd" ]]; then
      rm -rf $NXF_HOME/framework/$NXF_VER || exit $?
      $0 -version || exit $?
      exit 0
      fi
      ;;
    -self-update|self-update)
      if [[ ! "$cmd" ]]; then
      install $0;
      exit 0
      fi
      ;;
    -process.executor|-executor.name)
      if [[ $2 && $2 == 'gridgain' ]]; then
      NXF_MODE='gridgain'; shift;
      fi
      ;;
    -with-extrae)
      export EXTRAE_CONFIG_FILE=${EXTRAE_CONFIG_FILE:-$NXF_HOME/extrae/config}
      rm -f TRACE.*
      rm -rf set-0
      ;;
    -with-drmaa)
      if [[ $2 && $2 != -* ]];
      then NXF_DRMAA=$2; shift;
      else NXF_DRMAA='us.levk:drmaa-gridengine:6.2u5'; fi
      ;;
    *)
      [[ $1 && $1 != -* && ! "$cmd" && ${cli[*]} =~ $1 ]] && cmd=$1
      ;;
    esac
    shift
done

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_HOME/framework/$NXF_VER/$NXF_JAR}
NXF_BASE=${NXF_BASE:-http://www.nextflow.io/releases}
NXF_PATH=$(dirname "$NXF_BIN")
NXF_URL=${NXF_URL:-$NXF_BASE/v$NXF_VER/$NXF_JAR}
NXF_GRAB=${NXF_GRAB:-''}
NXF_CLASSPATH=${NXF_CLASSPATH:-''}
NXF_LAUNCHER=${NXF_HOME}/tmp/launcher/nextflow-${NXF_PACK}_${NXF_VER}

# 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

# 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 1.7+)/bin/java"
    else
        JAVA_CMD="$(which java)"
    fi
fi

# Verify installed Java version
if [ ! -d "$NXF_LAUNCHER" ]; then # <-- only the first time
    $JAVA_CMD -version 2>&1 | awk '/version/ {print $3}' | grep '"1\.[7|8]\..*"' > /dev/null
    if [ $? -ne 0 ]; then
         echo_red "Error: cannot find Java or it's a wrong version -- please make sure that Java 7 or higher it's installed"
         echo_red "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"
         exit 1
    fi
fi

# Verify nextflow jar is available
if [ ! -f "$NXF_BIN" ]; then
    [ -f "$NXF_PATH" ] && rm "$NXF_PATH"
    mkdir -p $NXF_PATH || exit $?
    get "$NXF_URL" "$NXF_BIN"
fi

check=".+:.+:.+"
if [[ "$NXF_DRMAA" =~ $check ]]; then
  # add drmaa library downloadable from maven to dependencies list
  NXF_GRAB+=" $NXF_DRMAA"
  NXF_MODE='drmaa'
elif [[ "$NXF_DRMAA" && -f "$NXF_DRMAA" ]]; then
  # add drmaa jar file to custom classpath
  NXF_CLASSPATH+=":$NXF_DRMAA"
  NXF_MODE='drmaa'
elif [[ "$NXF_DRMAA" ]]; then
  echo_red "Cannot find specified DRMAA library file: $NXF_DRMAA"
  exit 1
fi

[[ "$cmd" == "console" ]] && NXF_MODE='console'
[[ "$cmd" == "node" && ! "$NXF_MODE" ]] && NXF_MODE='gridgain'

COLUMNS=${COLUMNS:-`tty -s && tput cols 2>/dev/null || true`}
JAVA_OPTS="-noverify -Dcapsule.trampoline -Dcapsule.java.cmd=$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
[[ "${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_OPTS
$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
LAUNCH_FILE="${NXF_LAUNCHER}/classpath-$(env_md5)"
if [ -s "$LAUNCH_FILE" ] && [ "$LAUNCH_FILE" -nt "$NXF_BIN" ]; then
    launcher=($(cat "$LAUNCH_FILE"))
else
    # otherwise run the capsule and get the result classpath in the 'launcher' and save it to a file
    launcher=($("$JAVA_CMD" $JAVA_OPTS -jar "$NXF_BIN"))
    [[ $? -ne 0 ]] && echo 'Unable to initialize nextflow environment' && exit $?
    mkdir -p ${NXF_LAUNCHER}
    echo "${launcher[@]}" > "$LAUNCH_FILE"
fi

# finally run it
launch_nextflow