xworkStripes

#!/bin/bash
#
# xworkStripes:  a little script to make working with GoSTRIPES easier ...
#              Alls this does is to set the variable rws (run with singularity)
#              so that you can run commands from the GoSTRIPES container by
#              simply preceding them with $rws .
#
# Last update: December 12, 2018.  Volker Brendel.
#

boundDirset=0
imageset=0
alliswell=1

OPTIND=1
while getopts "b:i:" optname
  do
    case "$optname" in
      "b")
        boundDirset=1
        boundDir=$OPTARG
        ;;
      "i")
        imageset=1
        GoSTRIPESimage=$OPTARG
        ;;
      "?")
        echo "Unknown option $OPTARG."
        ;;
      ":")
        echo "No argument value provided for option $OPTARG."
        ;;
      *)
      # Bad luck!?:
        echo "An unknown error occurred while processing options."
        ;;
    esac
  done

if [[ $boundDirset == 0 || $imageset == 0 ]]
  then
    echo ""
    echo "USAGE: source xworkSTRIPES -b boundDir -i GoSTRIPESimage"
    echo ""
    echo "Required arguments:"
    echo ""
    echo "        boundDir = your working directory, accessible to GoSTRIPES"
    echo "        GoSTRIPESimage = full path to the GoSTRIPES Singularity image"
    echo ""
    echo "If you see this message, then something was not quite right."
    echo "  boundDIR was set to: $boundDIR."
    echo "  GoSTRIPESimage was set to: $GoSTRIPESimage."
    echo ""
    alliswell=0
fi

if [[ $alliswell == 1 ]]
  then
    echo ""
    echo ""
    echo "Ready to go STRIPES!"
    echo ""
    echo "Your current directory:"
    echo "$HOSTNAME"; pwd; echo""; date; echo""
    rws="singularity exec -e -B $boundDir $GoSTRIPESimage"

    echo "The rws variable has been set to:  $rws"
    echo 'Run a command within the GoSTRIPES container by preceding it with $rws.'
    echo ""
    echo "Example:"
    echo " which fastq-interleave"
    echo "will show you if you have fastq-interleave on your host system."
    echo ' $rws fastq-interleave'
    echo "will show you help information for the program, already installed in the GoSTRIPES image."
    echo ""
    echo "NOTE: You must invoke xworkStripes with 'source'."
    echo '      Otherwise $rws will not be available in your shell.'
    echo '      You might consider setting $rws as an enviroment variable.'
    echo '      Another approach is to set rws as an alias.'
    export rws
fi