Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
branch: master
Fetching contributors…

Cannot retrieve contributors at this time

executable file 73 lines (61 sloc) 2.002 kb
#!/bin/sh -
#
# This script reads and writes entries from a database.
# Examples:
# writedb_entry -help
# writedb_entry -s Pf3D7_01 Pf3D7_05 Pf3D7_07
#
#if [ -z "$ARTEMIS_HOME" ]; then
# PRG=`readlink -f "$0"`
# echo $PRG
# ARTEMIS_HOME=`dirname "$PRG"`/..
#fi
PRG=$0
progname=`basename $0`
while [ -h "$PRG" ] ; do
ls=`ls -ld "$PRG"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '.*/.*' > /dev/null; then
PRG="$link"
else
PRG="`dirname $PRG`/$link"
fi
done
ARTEMIS_HOME=`dirname "$PRG"`/..
CLASSPATH="$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:$ARTEMIS_HOME/lib/postgresql-8.4-701.jdbc3.jar:$ARTEMIS_HOME/lib/chado-14-interface.jar:$CLASSPATH"
CLASSPATH="$ARTEMIS_HOME/lib/commons-lang-2.6.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:$ARTEMIS_HOME/lib/retrotranslator-runtime-1.1.0.jar"
CLASSPATH="$CLASSPATH:$ARTEMIS_HOME/lib/picard/picard.jar"
export CLASSPATH
FLAGS="-mx2048m -ms20m -Djdbc.drivers=org.postgresql.Driver -Dibatis"
DEFAULT_CONNECTION="-Dchado=db.genedb.org:5432/snapshot?genedb_ro -Dread_only"
while test $# != 0
do
case $1 in
-Dchado*)
DEFAULT_CONNECTION="$1" ;;
-D*)
FLAGS="$FLAGS $1" ;;
*) break ;;
esac
shift
done
# searches for the -c option (needs to know the index)
idx=0
for arg in "$@"
do
if [ '-c' == "${arg}" ]; then
let "nextID = $idx + 1";
DEFAULT_CONNECTION="-Dchado=${!nextID}"
fi
if [ '-l' == "${arg}" ]; then
let "nextID = $idx + 2";
eval MAPPING_PATH="${!nextID}"
CLASSPATH="${MAPPING_PATH}:$CLASSPATH"
export CLASSPATH
fi
let idx++
done
echo starting to write with flags: $DEFAULT_CONNECTION $FLAGS 1>&2
java $DEFAULT_CONNECTION $FLAGS uk.ac.sanger.artemis.io.ReadAndWriteEntry "$@"
Jump to Line
Something went wrong with that request. Please try again.