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#!/bin/sh
#shell script that sets the CLASSPATH for the biojava classes
#and runs the alien_hunter.pl script with the user arguments
#author George Vernikos <gsv(at)sanger.ac.uk>
#LICENSE
#This program is free software; you can redistribute it and/or
#modify it under the terms of the GNU General Public License
#as published by the Free Software Foundation; either version 2
#of the License, or (at your option) any later version.
#
#This program is distributed in the hope that it will be useful,
#but WITHOUT ANY WARRANTY; without even the implied warranty of
#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#GNU General Public License for more details.
#You should have received a copy of the GNU General Public License
#along with this program; if not, write to the Free Software
#Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
#$1 sequence file
#$2 output
#$3 -a | -c | -i
#$4 -a | -c | -i
#$5 -a | -c | -i
USERPATH=/usr/share/alien_hunter
#CLASSPATH=${CLASSPATH}:$USERPATH/biojava/biojava-1.4_new.jar
#CLASSPATH=${CLASSPATH}:$USERPATH/biojava/commons-cli.jar
#CLASSPATH=${CLASSPATH}:$USERPATH/biojava/commons-collections-2.1.jar
#CLASSPATH=${CLASSPATH}:$USERPATH/biojava/commons-dbcp-1.1.jar
#CLASSPATH=${CLASSPATH}:$USERPATH/biojava/commons-pool-1.1.jar
#CLASSPATH=${CLASSPATH}:$USERPATH/biojava/bytecode-0.92.jar
CLASSPATH=${CLASSPATH}:$USERPATH/
export CLASSPATH
perl $USERPATH/alien_hunter.pl -f $1 -o $2 $3 $4 $5
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