#!/bin/sh -

# this script will run a search program on a sequence input file or on each
# file in a file of filenames

# to customise this script see the function called run_one_prog below


RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_netblastp,v 1.1 2008-12-01 08:52:51 tjc Exp $"

PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`


if [ $# = 4 -a x$1 = x-onefile ]
then
    shift
    ONEFILE=t
    DATABASE=$3 export DATABASE
else
    if [ $# = 2 ]
    then
        DATABASE=$2 export DATABASE
    else
        echo usage: $0 -onefile input_file output_file database
        echo    or: $0 file_of_filenames database
        exit 1
    fi
fi


# expand any ~ or environment variables
EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`


### change this function to suit your site:

run_one_prog () {
    INPUT_FILE=$1
    OUTPUT_FILE=$2
    DATABASE=$3


    ### change these lines:
    
    EXEC=${EXEC-`which $PROG 2>/dev/null`}
    
    #
    # Mac specific - NCBI .dmg installation area
    #
    PLATTMP=`uname`
	if [ "$PLATTMP" = "Darwin" ] && [ "$EXEC" = "" ] && [ -x /usr/local/ncbi/blast/bin/$PROG ]
	then
		EXEC=/usr/local/ncbi/blast/bin/$PROG
    fi
    
    if [ ! -x "$EXEC" ]
    then
    	echo "ERROR: Cannot find an executable $PROG blast program. Exiting."
    	exit 1
    fi


	# Use remote flag for a NCBI command line search...
    COMMAND="$EXEC -db $DATABASE -query $INPUT_FILE -remote"
	
	echo
	echo "input file: $INPUT_FILE"
	echo "output will be written to: $OUTPUT_FILE"
	echo "executing command: $COMMAND" 1>&2
	
    # add/change the flags to suit your site:
    nice -n 19 $COMMAND 2>&1 > $OUTPUT_FILE | tee ${PROG}_errors.new 1>&2

    #### end of changes


    # Artemis can read compressed files
    gzip -9 $OUTPUT_FILE &

    if [ -s ${PROG}_errors.new ]
    then
        ( echo ERROR running $PROG: ; echo; 
          echo ===================================================
          cat ${PROG}_errors.new ) >> $OUTPUT_FILE
        cat ${PROG}_errors.new >> ${PROG}_errors
    fi
}

(echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill

chmod a+x $PROG.kill

if [ x$ONEFILE = x ]
then
    for i in `cat $1`
    do
        run_one_prog $i $i.out $EXPANDED_DATABASE
    done

else
    run_one_prog $1 $2 $EXPANDED_DATABASE
fi

exit 0
