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#!/bin/sh -
#
# This script reads and writes entries from a database.
# Examples:
# writedb_entry -help
# writedb_entry -s Pf3D7_01 Pf3D7_05 Pf3D7_07
#
args="$*"
ARTEMIS_HOME=/software/pathogen/projects/artemis/current/
ARTEMIS_HOME=/software/pathogen/projects/artemis/test/
CLASSPATH=$ARTEMIS_HOME:$ARTEMIS_HOME/lib/biojava.jar:$ARTEMIS_HOME/lib/jemAlign.jar:$ARTEMIS_HOME/lib/jakarta-regexp-1.2.jar:$ARTEMIS_HOME/lib/macos.jar:$ARTEMIS_HOME/lib/postgresql-8.1-407.jdbc2ee.jar:$ARTEMIS_HOME/lib/chado-14-interface.jar:$CLASSPATH
# iBatis jars
CLASSPATH=$CLASSPATH:$ARTEMIS_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$ARTEMIS_HOME/lib/ibatis/:$ARTEMIS_HOME/lib/ibatis/log4j-1.2.14.jar:$ARTEMIS_HOME/lib/ibatis/cglib-nodep-2.2.jar:$ARTEMIS_HOME/lib/retrotranslator-runtime-1.1.0.jar
export CLASSPATH
FLAGS="-mx512m -ms20m -Djdbc.drivers=org.postgresql.Driver -Dibatis"
DEFAULT_CONNECTION="-Dchado=pathdbsrv1-dmz.sanger.ac.uk:5432/snapshot?genedb_ro -Dread_only"
if [ $# = 0 ]
then
:
else
while test $# != 0
do
case $1 in
-Dchado*)
DEFAULT_CONNECTION="$1" ;;
-D*)
FLAGS="$FLAGS $1" ;;
*) break ;;
esac
shift
done
fi
echo starting to write with flags: $DEFAULT_CONNECTION $FLAGS 1>&2
java $DEFAULT_CONNECTION $FLAGS uk.ac.sanger.artemis.io.ReadAndWriteEntry $*