restore invocation

#####usage statement#####

#get shell

## detect shell across different OS

if [[ $VENDOR != "apple" ]]

    then

    SHELL=$(readlink -f /proc/$$/exe | cut -d'/' -f3)

else

    SHELL=$(ps -p $$ | awk '$1 == PP {print $4}' PP=$$)

fi

## detect how called (e.g., bash converrt.sh or ./launch_universc.sh)

if [[ $(which launch_universc.sh) != *"not found" ]]

    then

    SHELL='' 

    invocation=$0

if [[ -n $BASH_VERSION ]]; then

    invocation='bash '${invocation}''

elif [[ -n $ZSH_VERSION ]]; then

    invocation='zsh '${invocation}''

elif [[ -n $FISH_VERSION ]]; then

    invocation='fish '${invoaction}''

elif [[ -n $KSH_VERSION ]]; then

    invocation='ksh '${invocation}''

else

    if [[ -z $ZSH_VERSION ]]

        then

        SHELL="zsh"

    elif [[ -z $KSH_VERSION ]]

       then

       SHELL="ksh"

    elif [[ -z $FISH_VERSION ]]

       then

       SHELL="fish"

    elif [[ -z $BASH_VERSION ]]

        then

        SHELL="bash"

    else

       SHELL=$SHELL

    fi

    invocation=$(echo $(basename $0))

fi

#usage statement

help='

Usage:

  '$invocation' --testrun -t TECHNOLOGY

  '$invocation' -t TECHNOLOGY --setup

  '$invocation' -R1 FILE1 -R2 FILE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$invocation' -R1 READ1_LANE1 READ1_LANE2 -R2 READ2_LANE1 READ2_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$invocation' -f SAMPLE_LANE -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$invocation' -f SAMPLE_LANE1 SAMPLE_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$invocation' -v

  '$invocation' -h

  '$SHELL' '$invocation' --testrun -t TECHNOLOGY

  '$SHELL' '$invocation' -t TECHNOLOGY --setup

  '$SHELL' '$invocation' -R1 FILE1 -R2 FILE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -R1 READ1_LANE1 READ1_LANE2 -R2 READ2_LANE1 READ2_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -f SAMPLE_LANE -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -f SAMPLE_LANE1 SAMPLE_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -v

  '$SHELL' '$invocation' -h

Convert sequencing data (FASTQ) from Nadia or ICELL8 platforms for compatibility with 10x Genomics and run cellranger count