#!/bin/bash

odir=$1

fafile=$2

fqfile=$3

if [ $# -lt 3 ] || [ $1 == '-h' ]; then

echo; echo " Usage:" \$MYSMISDIR/$(basename $0) \</full/path/to/destdir\> \<draft_assembly\> \<long_reads\> ; echo

echo " /full/path/to/destdir: folder where to run the pipeline (Please provide full path)"

echo " draft_assembly: fasta file of the assembly to be scaffolded (Please provide full path)"

echo " long_reads: fastq file of long reads for scaffolding (Please provide full path)"

exit 1

fi

echo; echo "${MYSMISDIR:?Need to set MYSMISDIR to location of your smis}" > /dev/null

mkdir -p $odir

cd $odir

rm -f mysettings.sh

echo export "MYSMISDIR="$MYSMISDIR > mysettings.sh

sed -e "s#ODIR#$odir#g" $MYSMISDIR/settings.sh \

| sed -e "s#FAFILE#$fafile#g" | sed -e "s#FQFILE#$fqfile#g" >> mysettings.sh

sed "s#ODIR#$odir#g" $MYSMISDIR/smissv.sh > mysmissv.sh

chmod x mysmissv.sh

echo

echo " You're all set! You can now launch $odir/mysmissv.sh to run the pipeline:"

echo " $ cd "$odir

echo " $ ./mysmissv.sh"

echo; echo " If needed, modify alignment and scaffolding settings in file $odir/mysettings.sh"

echo