nextflow

#!/bin/bash
#
#  Copyright (c) 2013-2014, Centre for Genomic Regulation (CRG).
#  Copyright (c) 2013-2014, 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 && $TERM != 'dumb' ]]; then
NORMAL=$(tput sgr0)
GREEN=$(tput setaf 2; tput bold)
YELLOW=$(tput setaf 3)
RED=$(tput setaf 1)
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 --tmpdir=$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 ''
}

# 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=${NXF_VER:-'0.12.0'}
NXF_ORG=${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 args=("$@")
declare -a cli=(clone config drop help history info ls pull run view node console)
cmd=''
while [[ $# != 0 ]]; do
    case $1 in
    -bg)
      bg=1
      ;;
    -download)
      if [[ ! "$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 && $2 == 'gridgain' ]]; then
      NXF_PACKAGE='gg'; shift;
      fi
      ;;
    -with-extrae)
      export EXTRAE_CONFIG_FILE=${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

[[ "$cmd" == "console" ]] && NXF_PACKAGE='console'
[[ "$cmd" == "node" && ! "$NXF_PACKAGE" ]] && NXF_PACKAGE='gg'

NXF_PACKAGE=${NXF_PACKAGE:-one}
NXF_JAR=${NXF_JAR:-nextflow-$NXF_VER-$NXF_PACKAGE.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:-''}

# define the path when dependencies jars will be extracted
export CAPSULE_CACHE_DIR=${CAPSULE_CACHE_DIR:=$NXF_HOME/capsule}
CAPSULE_LOG=${CAPSULE_LOG:-'none'}

# 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
    else
        JAVA_CMD="`which java`"
    fi
fi

# Verify installed Java version
if [ ! -f "$NXF_BIN" ]; 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

    [ -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+=" $NXF_DRMAA"
elif [[ "$NXF_DRMAA" && -f "$NXF_DRMAA" ]]; then
  # add drmaa jar file to custom classpath
  NXF_CLASSPATH+=":$NXF_DRMAA"
elif [[ "$NXF_DRMAA" ]]; then
  echo_red "Cannot find specified DRMAA library file: $NXF_DRMAA"
  exit 1
fi

COLUMNS=${COLUMNS:-`tty -s && tput cols 2>/dev/null || true`}
JAVA_OPTS="-noverify -Dcapsule.trampoline"
if [[ $cmd == console ]]; then bg=1;
else JAVA_OPTS+=" -Djava.awt.headless=true"
fi
[[ "$JAVA_HOME" ]] && JAVA_OPTS+=" -Dcapsule.java.home=$JAVA_HOME"
[[ "$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
# 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

# Start in daemon mode
if [[ "$bg" ]]; then
  NXF_PID_FILE=${NXF_PID_FILE:-'.nextflow.pid'}
  `"$JAVA_CMD" $JAVA_OPTS -jar "$NXF_BIN"` "${args[@]}" &
  disown
  printf $! > $NXF_PID_FILE
  exit 0
fi

exec `"$JAVA_CMD" $JAVA_OPTS -jar "$NXF_BIN"` "${args[@]}"
exit 1