mfold

mfold

#!/bin/sh
# This shell script folds an RNA or DNA sequence and creates output
# files.
export ZUKER_URL="http://www.bioinfo.rpi.edu/%7Ezukerm/"
export DATDIR=${MFOLDDAT:-$MFOLD/dat}
export IMG_DIR=$DATDIR


# Abort subroutine
abort(){
    \rm -f mfold.log  fort.*
    if [ $# -gt 0 ] ; then
	    echo -e "$1"
    fi
    echo "Job Aborted"
    exit 1
	}
	
if [ $DATDIR = "/dat" ] ; then
    abort "The environment variable, MFOLDDAT, is not set."
fi

if [ $# = 0 ]
	then
    echo -e "Usage is\nmfold SEQ='file_name' with optional parameters:
    [ AUX='auxfile_name' ] [ RUN_TYPE=text (default) or html ]
    [ NA=RNA (default) or DNA ] [ LC=sequence type (default = linear) ]
    [ T=temperature (default = 37