<commit_before>#!/bin/bash
#
# Copyright (c) 2013-2016, Centre for Genomic Regulation (CRG).
# Copyright (c) 2013-2016, <NAME> 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/>.
#

#set -e
#set -u
#set -o errexit

# the application 'base' folder
bin_dir=`dirname "$0"`
bin_dir=`cd "$bin_dir"; pwd`
base_dir=$bin_dir

# define the java env
java=java
if test -n "$JAVA_HOME"; then
	java="$JAVA_HOME/bin/java"
fi

#
# debugging JVM options
#  export _JAVA_OPTIONS='-Xms1g -Xmx2g -verbose:gc -XX:+AggressiveOpts -XX:+UnlockDiagnosticVMOptions -XX:+UnlockExperimentalVMOptions -XX:+PrintFlagsFinal -XX:+TraceClassLoading -XX:+TraceClassUnloading -verbose:class'
#

#
# Variable definition
#
declare -a args=()
DEBUG=''
COLUMNS=${COLUMNS:-`tput cols 2> /dev/tty`}
MAIN_CLASS=${MAIN_CLASS:-'nextflow.cli.Launcher'}
JVM_ARGS+=" -Dfile.encoding=UTF-8 -noverify -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
## flight recorded -- http://docs.oracle.com/javacomponents/jmc-5-4/jfr-runtime-guide/run.htm
##JVM_ARGS+=" -XX:+UnlockCommercialFeatures -XX:+FlightRecorder -XX:StartFlightRecording=duration=60s,filename=myrecording.jfr"
NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
NXF_OPTS=${NXF_OPTS:-}
EXTRAE_CONFIG_FILE=${EXTRAE_CONFIG_FILE:-$NXF_HOME/extrae/config}
NXF_CLI="$0 $@"
export NXF_CLI
export COLUMNS
export EXTRAE_CONFIG_FILE

DRIP_INIT_CLASS=nextflow.cli.DripMain
DRIP_INIT=''

EXTRAE_CONFIG_FILE=${EXTRAE_CONFIG_FILE:-$NXF_HOME/extrae/config}

#
# classpath when the application is compiled with gradle
#
if [ -e "$base_dir/build/libs" ]; then
  CLASSPATH=`ls $base_dir/build/libs/* | egrep 'nextflow-[0-9]+\.[0-9]+\.[0-9]+(-[A-Z0-9]+)?.jar$'`

  # -- append runtime libraries
  [[ ! -f "$base_dir/.launch.classpath" ]] && echo "Missing '.launch.classpath' file -- create it by running: ./gradlew exportClasspath" && exit 1<commit_msg>Fixed launcher version number containing lowercase characters <commit_after>#!/bin/bash
#
# Copyright (c) 2013-2016, Centre for Genomic Regulation (CRG).
# Copyright (c) 2013-2016, <NAME> 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/>.
#

#set -e
#set -u
#set -o errexit

# the application 'base' folder
bin_dir=`dirname "$0"`
bin_dir=`cd "$bin_dir"; pwd`
base_dir=$bin_dir

# define the java env
java=java
if test -n "$JAVA_HOME"; then
	java="$JAVA_HOME/bin/java"
fi

#
# debugging JVM options
#  export _JAVA_OPTIONS='-Xms1g -Xmx2g -verbose:gc -XX:+AggressiveOpts -XX:+UnlockDiagnosticVMOptions -XX:+UnlockExperimentalVMOptions -XX:+PrintFlagsFinal -XX:+TraceClassLoading -XX:+TraceClassUnloading -verbose:class'
#

#
# Variable definition
#
declare -a args=()
DEBUG=''
COLUMNS=${COLUMNS:-`tput cols 2> /dev/tty`}
MAIN_CLASS=${MAIN_CLASS:-'nextflow.cli.Launcher'}
JVM_ARGS+=" -Dfile.encoding=UTF-8 -noverify -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
## flight recorded -- http://docs.oracle.com/javacomponents/jmc-5-4/jfr-runtime-guide/run.htm
##JVM_ARGS+=" -XX:+UnlockCommercialFeatures -XX:+FlightRecorder -XX:StartFlightRecording=duration=60s,filename=myrecording.jfr"
NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
NXF_OPTS=${NXF_OPTS:-}
EXTRAE_CONFIG_FILE=${EXTRAE_CONFIG_FILE:-$NXF_HOME/extrae/config}
NXF_CLI="$0 $@"
export NXF_CLI
export COLUMNS
export EXTRAE_CONFIG_FILE

DRIP_INIT_CLASS=nextflow.cli.DripMain
DRIP_INIT=''

EXTRAE_CONFIG_FILE=${EXTRAE_CONFIG_FILE:-$NXF_HOME/extrae/config}

#
# classpath when the application is compiled with gradle
#
if [ -e "$base_dir/build/libs" ]; then
  CLASSPATH=`ls $base_dir/build/libs/* | egrep 'nextflow-[0-9]+\.[0-9]+\.[0-9]+(-[a-zA-Z0-9]+)?.jar$'`

  # -- append runtime libraries
  [[ ! -f "$base_dir/.launch.classpath" ]] && echo "Missing '.launch.classpath' file -- create it by running: ./gradlew exportClasspath" && exit 1
{'fraction_non_alphanumeric': 0.136417791898332, 'fraction_numerical': 0.014694201747418586, 'mean_word_length': 4.863795110593713, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 9, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3537612', 'n_tokens_mistral': 1870, 'n_tokens_neox': 1792, 'n_words': 468}