createTessNLPJobs.sh

# should be run from ChtcRun directory
# needs to: 
    # create submit dir
    # set up proper shared/ stuff
    # loop over _out dirs, copying tess*.hocr over
    # run mkdag

# clean up journal name, removing commas and spaces
journal=$1
journal_clean=${journal//,/}
journal_clean=${journal_clean// /_}
journal_out="$journal_clean"_out
journal_new="$journal_clean"_NLP

for job in "$journal_out"/job*/;
do
    if ls $job/*hocr.html 1> /dev/null 2>&1; then
        mkdir -p $journal_new${job/$journal_out/}
        ln -s `pwd`/$job/*hocr.html $journal_new${job/$journal_out/}
    fi
done

# assume ChtcRun/NLPshared exists and holds all common shared junk
cp -r NLPshared $journal_new
mv $journal_new/NLPshared $journal_new/shared
echo "Submit directories created from requested output! Use mkdag to create DAG files for submission. e.g.:"
echo ./mkdag --cmdtorun=do.sh --data=$journal_new --outputdir="$journal_new"_out_NLP --pattern=SUCCEED.txt --type=other